public void AutomatedRefresh(cDescriptorType CurrentDescriptorType, bool IsFullScreen)
{
if (IsFullScreen == false)
{
cExtendedTable MinMax = this.AssociatedPlate.GetMinMax(CurrentDescriptorType);
this.GeneralMin = MinMax[0][0];
this.GeneralMax = MinMax[0][1];
}
}
public FormForDescriptorInfo(cDescriptorType CurrentDesc)
{
this.CurrentDesc = CurrentDesc;
InitializeComponent();
this.textBoxNameDescriptor.Text = CurrentDesc.GetName();
this.richTextBoxDescription.Text = CurrentDesc.description;
this.labelDataType.Text = CurrentDesc.GetDataType();
if (CurrentDesc.GetDataType() == "Single")
this.numericUpDownBinValue.Visible = false;
this.numericUpDownBinValue.Value = CurrentDesc.GetBinNumber();
this.OriginalBinNumber = CurrentDesc.GetBinNumber();
if (CurrentDesc.IsConnectedToDatabase)
{
this.labelDataBaseConnection.Text = "DataBase Connection.";
panelForColor.BackColor = Color.LightGreen;
}
else
{
this.labelDataBaseConnection.Text = "No DataBase connection.";
panelForColor.BackColor = Color.Red;
}
}
private void RatioPopDescItem(object sender, EventArgs e)
{
cGUI_2ClassesSelection GUI_ListClasses = new cGUI_2ClassesSelection();
GUI_ListClasses.ClassType = eClassType.PHENOTYPE;
GUI_ListClasses.PanelRight_IsCheckBoxes = true;
GUI_ListClasses.PanelLeft_IsCheckBoxes = true;
if (GUI_ListClasses.Run(this.GlobalInfo).IsSucceed == false) return;
List<cCellularPhenotype> LCP0 = new List<cCellularPhenotype>();
List<cCellularPhenotype> LCP1 = new List<cCellularPhenotype>();
for (int IdxPheno = 0; IdxPheno < GUI_ListClasses.GetOutPut()[0].Count; IdxPheno++)
{
if (GUI_ListClasses.GetOutPut()[0][IdxPheno] == 1)
LCP0.Add(cGlobalInfo.ListCellularPhenotypes[IdxPheno]);
if (GUI_ListClasses.GetOutPut()[1][IdxPheno] == 1)
LCP1.Add(cGlobalInfo.ListCellularPhenotypes[IdxPheno]);
}
//if (LCP.Count == 0) return;
string description = "Ratio of:\n";
foreach (var item in LCP0)
description += item.Name + "\n";
description += "over\n";
foreach (var item in LCP1)
description += item.Name + "\n";
cDescriptorType NewAverageType = new cDescriptorType("Ratio_Pop", true, 1, description);
cGlobalInfo.CurrentScreening.ListDescriptors.AddNew(NewAverageType);
FormForProgress ProgressWindow = new FormForProgress();
ProgressWindow.Show();
int IdxProgress = 0;
int MaxProgress = 0;
foreach (cPlate CurrentPlateToProcess in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
MaxProgress += (int)CurrentPlateToProcess.ListWells.Count;
ProgressWindow.progressBar.Maximum = MaxProgress;
foreach (cPlate TmpPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
foreach (cWell Tmpwell in TmpPlate.ListWells)
{
TmpPlate.DBConnection = new cDBConnection(TmpPlate, Tmpwell.SQLTableName);
List<cDescriptorType> LDT = new List<cDescriptorType>();
LDT.Add(cGlobalInfo.CurrentScreening.ListDescriptors[0]);
cExtendedTable CT = TmpPlate.DBConnection.GetWellValues(Tmpwell, LDT, LCP0, 1);
double NumObject0 = CT[0].Count;
cExtendedTable CT1 = TmpPlate.DBConnection.GetWellValues(Tmpwell, LDT, LCP1, 1);
double NumObject1 = CT1[0].Count;
cListSignature LDesc = new cListSignature();
double Value = 0;
if (NumObject1 == 0)
Value = 0;
else
Value = NumObject0 / NumObject1;
cSignature NewDesc = new cSignature(Value, NewAverageType, cGlobalInfo.CurrentScreening);
LDesc.Add(NewDesc);
Tmpwell.AddSignatures(LDesc);
TmpPlate.DBConnection.CloseConnection();
ProgressWindow.richTextBoxForComment.AppendText(TmpPlate.GetName() + " : " + Tmpwell.GetShortInfo().Remove(Tmpwell.GetShortInfo().Length - 2) + "\n");
ProgressWindow.progressBar.Value = IdxProgress++;
ProgressWindow.Refresh();
}
}
ProgressWindow.Close();
cGlobalInfo.CurrentScreening.ListDescriptors.UpDateDisplay();
cGlobalInfo.CurrentScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; idxP++)
cGlobalInfo.CurrentScreening.ListPlatesActive[idxP].UpDataMinMax();
}
public cExtendedTable GetWellValues(cWell TmpWell, cDescriptorType DescType)
{
List<cDescriptorType> LCDT = new List<cDescriptorType>();
LCDT.Add(DescType);
cExtendedTable ToReturn = new cExtendedTable(this.GetWellValues(TmpWell, LCDT));
cListSingleBiologicalObjects ListClassesPhenotypes =
this.GetBiologicalPhenotypes(/*this.GetWellValues(TmpWell.SQLTableName, DescType),*/ TmpWell);
for (int i = 0; i < ToReturn.Count; i++)
{
ToReturn[i].ListTags = new List<object>();
for (int j = 0; j < ListClassesPhenotypes.Count; j++)
ToReturn[i].ListTags.Add(ListClassesPhenotypes[j]);
}
return ToReturn;
}
public string GeneratePCADescriptor(cListPlates PlatesToProcess, int NumberOfAxis, int NeutralClass)
{
int NumWell = 0;
int NumWellForLearning = 0;
foreach (cPlate CurrentPlate in PlatesToProcess)
{
NumWellForLearning += CurrentPlate.GetNumberOfWellOfClass(NeutralClass);
NumWell += cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().GetNumberOfActiveWells();
}
if (NumWellForLearning == 0)
{
MessageBox.Show("No well identified !", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return null;
}
int NumDesc = cGlobalInfo.CurrentScreening.GetNumberOfActiveDescriptor();
if (NumDesc <= 1)
{
MessageBox.Show("More than one descriptor are required for this operation", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return null;
}
double[,] DataForLDA = new double[NumWellForLearning, cGlobalInfo.CurrentScreening.GetNumberOfActiveDescriptor() + 1];
// return;
Matrix EigenVectors = PCAComputation(DataForLDA, NumWellForLearning, NumDesc, NeutralClass, PlatesToProcess);
string AxeName = "";
int IDxDesc = 0;
//for (int Desc = 0; Desc < CompleteScreening.ListDescriptors.Count; Desc++)
//{
// if (CompleteScreening.ListDescriptors[Desc].IsActive() == false) continue;
// AxeName += String.Format("{0:0.##}", EigenVectors.getElement(CompleteScreening.ListDescriptors.Count - 1, 0)) + "x" + CompleteScreening.ListDescriptorName[CompleteScreening.ListDescriptors.Count - 1];
//}
int OriginalDescNumber = cGlobalInfo.WindowHCSAnalyzer.checkedListBoxActiveDescriptors.Items.Count;
for (int AxesIdx = 0; AxesIdx < NumberOfAxis; AxesIdx++)
{
//for (int Idx = 0; Idx < CompleteScreening.GlobalInfo.WindowHCSAnalyzer.checkedListBoxActiveDescriptors.Items.Count; Idx++)
//{
// if (CompleteScreening.ListDescriptors[Idx].IsActive())
// if (CompleteScreening.ListDescriptors[Idx].GetBinNumber() == 1)
// {
// AxeName += String.Format("{0:0.###}", EigenVectors.getElement(IDxDesc++, AxesIdx)) + "x" + CompleteScreening.ListDescriptors[Idx].GetName() + " + ";
// }
// else
// {
// MessageBox.Show("Descriptor length not consistent (" + CompleteScreening.ListDescriptors[Idx].GetName() + " : " + CompleteScreening.ListDescriptors[Idx].GetBinNumber() + " bins", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
// return "";
// }
//}
//cDescriptorsType ColumnType = new cDescriptorsType(AxeName.Remove(AxeName.Length - 3), true, 1);
cDescriptorType ColumnType = new cDescriptorType("PCA_" + (AxesIdx + 1), true, 1);
while (cGlobalInfo.CurrentScreening.ListDescriptors.AddNew(ColumnType) == false)
{
FormForNewDescName NewNameWindow = new FormForNewDescName();
NewNameWindow.textBoxName.Text = ColumnType.GetName();
if (NewNameWindow.ShowDialog() != System.Windows.Forms.DialogResult.OK)
return ColumnType.GetName();
ColumnType.ChangeName(NewNameWindow.textBoxName.Text);
}
//CompleteScreening.ListDescriptors.AddNew(ColumnType);
foreach (cPlate TmpPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
foreach (cWell Tmpwell in TmpPlate.ListActiveWells)
{
cListSignature LDesc = new cListSignature();
double NewValue = 0;
IDxDesc = 0;
// AxeName += "\nPCA_" + (AxesIdx + 1);
for (int Idx = 0; Idx < OriginalDescNumber - 1; Idx++)
{
if (cGlobalInfo.CurrentScreening.ListDescriptors[Idx].IsActive())
// AxeName += String.Format("{0:0.###}", EigenVectors.getElement(IDxDesc, AxesIdx)) + "x" + CompleteScreening.ListDescriptors[Idx].GetName() + " + ";
NewValue += EigenVectors.getElement(IDxDesc++, AxesIdx) * Tmpwell.ListSignatures[Idx].GetValue();
}
cSignature NewDesc = new cSignature(NewValue, ColumnType, cGlobalInfo.CurrentScreening);
LDesc.Add(NewDesc);
Tmpwell.AddSignatures(LDesc);
}
}
}
cGlobalInfo.CurrentScreening.ListDescriptors.UpDateDisplay();
cGlobalInfo.CurrentScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; idxP++)
cGlobalInfo.CurrentScreening.ListPlatesActive[idxP].UpDataMinMax();
StartingUpDateUI();
return AxeName;
}
private void AverageOperationsToDescriptorItem(object sender, EventArgs e)
{
FormForDescOperations MainWindow = new FormForDescOperations(cGlobalInfo.CurrentScreening.ListDescriptors.GetListNames());
MainWindow.Text = "Average Based Operations";
if (MainWindow.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
string NewDescName = MainWindow.textBoxNewDescName.Text;
cDescriptorType DescType1 = cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorByName(MainWindow.comboBoxDescriptor1.Text);
cDescriptorType DescType2 = cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorByName(MainWindow.comboBoxDescriptor2.Text);
if ((DescType1 == null) || (DescType2 == null)) return;
FormForProgress ProgressWindow = new FormForProgress();
ProgressWindow.Show();
int IdxProgress = 1;
int MaxProgress = cGlobalInfo.CurrentScreening.ListPlatesAvailable.Count;
ProgressWindow.progressBar.Maximum = MaxProgress;
cDescriptorType NewDescType = new cDescriptorType(NewDescName, true, 1);
cGlobalInfo.CurrentScreening.ListDescriptors.AddNew(NewDescType);
eBinaryOperationType PostProcessBinaryOp = eBinaryOperationType.UNDEFINED;
if (MainWindow.checkBoxActivePostProcess.Checked)
{
switch (MainWindow.domainUpDownPostProcessOperator.Text)
{
case "*":
PostProcessBinaryOp = eBinaryOperationType.MULTIPLY;
break;
case "+":
PostProcessBinaryOp = eBinaryOperationType.ADD;
break;
case "/":
PostProcessBinaryOp = eBinaryOperationType.DIVIDE;
break;
case "-":
PostProcessBinaryOp = eBinaryOperationType.SUBSTRACT;
break;
default:
return;
}
}
if (MainWindow.tabControlMain.SelectedTab.Name == "tabPageBinary")
{
// SingleCellOperation.ListDualOperations = new List<eBinaryOperationType>();
// eDualOperationType OperationType = eDualOperationType.ADD;
eBinaryOperationType BinaryOp = eBinaryOperationType.ADD;
switch (MainWindow.domainUpDown1.Text)
{
case "*":
BinaryOp = eBinaryOperationType.MULTIPLY;
break;
case "+":
BinaryOp = eBinaryOperationType.ADD;
break;
case "/":
BinaryOp = eBinaryOperationType.DIVIDE;
break;
case "-":
BinaryOp = eBinaryOperationType.SUBSTRACT;
break;
default:
return;
}
foreach (cPlate CurrentPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
foreach (cWell Tmpwell in CurrentPlate.ListActiveWells)
{
cListSignature LDesc = new cListSignature();
cSignature NewDesc = null;
double Val = 0;
switch (BinaryOp)
{
case eBinaryOperationType.ADD:
Val = Tmpwell.GetAverageValue(DescType1) + Tmpwell.GetAverageValue(DescType2);
break;
case eBinaryOperationType.MULTIPLY:
Val = Tmpwell.GetAverageValue(DescType1) * Tmpwell.GetAverageValue(DescType2);
break;
case eBinaryOperationType.SUBSTRACT:
Val = Tmpwell.GetAverageValue(DescType1) - Tmpwell.GetAverageValue(DescType2);
break;
case eBinaryOperationType.DIVIDE:
double denominator = Tmpwell.GetAverageValue(DescType2);
if (denominator == 0) Val = 0;
else Val = Tmpwell.GetAverageValue(DescType1) / denominator;
break;
default:
break;
}
if (PostProcessBinaryOp != eBinaryOperationType.UNDEFINED)
{
double ValuePostProcess = (double)MainWindow.numericUpDownPostProcessValue.Value;
switch (PostProcessBinaryOp)
{
case eBinaryOperationType.ADD:
Val += ValuePostProcess;
break;
case eBinaryOperationType.SUBSTRACT:
Val -= ValuePostProcess;
break;
case eBinaryOperationType.MULTIPLY:
Val *= ValuePostProcess;
break;
case eBinaryOperationType.DIVIDE:
if (ValuePostProcess == 0)
Val = 0;
else
Val /= ValuePostProcess;
break;
default:
break;
}
}
NewDesc = new cSignature(Val, NewDescType, cGlobalInfo.CurrentScreening);
LDesc.Add(NewDesc);
Tmpwell.AddSignatures(LDesc);
}
ProgressWindow.progressBar.Value = IdxProgress++;
ProgressWindow.richTextBoxForComment.AppendText(CurrentPlate.GetShortInfo());
ProgressWindow.Refresh();
}
}
#region unary operator
else
{
eUnaryOperationType OperationType = eUnaryOperationType.LOG;
if (MainWindow.radioButtonSQRT.Checked)
OperationType = eUnaryOperationType.SQRT;
else if (MainWindow.radioButtonLog.Checked)
OperationType = eUnaryOperationType.LOG;
else if (MainWindow.radioButtonABS.Checked)
OperationType = eUnaryOperationType.ABS;
else if (MainWindow.radioButtonEXP.Checked)
OperationType = eUnaryOperationType.EXP;
foreach (cPlate CurrentPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
foreach (cWell Tmpwell in CurrentPlate.ListActiveWells)
{
cListSignature LDesc = new cListSignature();
cSignature NewDesc = null;
double Val = 0;
switch (OperationType)
{
case eUnaryOperationType.LOG:
Val = Math.Log(Tmpwell.GetAverageValue(DescType1));
if (double.IsInfinity(Val) || double.IsNaN(Val)) Val = double.Epsilon;
break;
case eUnaryOperationType.SQRT:
Val = Tmpwell.GetAverageValue(DescType1);
if (Val < 0) Val = 0;
Val = Math.Sqrt(Val);
break;
case eUnaryOperationType.ABS:
Val = Math.Abs(Tmpwell.GetAverageValue(DescType1));
break;
case eUnaryOperationType.EXP:
Val = Math.Exp(Tmpwell.GetAverageValue(DescType1));
break;
default:
break;
}
if (PostProcessBinaryOp != eBinaryOperationType.UNDEFINED)
{
double ValuePostProcess = (double)MainWindow.numericUpDownPostProcessValue.Value;
switch (PostProcessBinaryOp)
{
case eBinaryOperationType.ADD:
Val += ValuePostProcess;
break;
case eBinaryOperationType.SUBSTRACT:
Val -= ValuePostProcess;
break;
case eBinaryOperationType.MULTIPLY:
Val *= ValuePostProcess;
break;
case eBinaryOperationType.DIVIDE:
if (ValuePostProcess == 0)
Val = 0;
else
Val /= ValuePostProcess;
break;
default:
break;
}
}
NewDesc = new cSignature(Val, NewDescType, cGlobalInfo.CurrentScreening);
LDesc.Add(NewDesc);
Tmpwell.AddSignatures(LDesc);
}
ProgressWindow.progressBar.Value = IdxProgress++;
ProgressWindow.richTextBoxForComment.AppendText(CurrentPlate.GetShortInfo());
ProgressWindow.Refresh();
}
}
#endregion
ProgressWindow.Close();
int IdxNull = 0;
foreach (cPlate TmpPlate in cGlobalInfo.CurrentScreening.ListPlatesActive)
{
foreach (cWell TmpWell in TmpPlate.ListActiveWells)
if (TmpWell.ListSignatures.Count != cGlobalInfo.CurrentScreening.ListDescriptors.Count)
IdxNull++;
}
if (IdxNull > 0)
System.Windows.Forms.MessageBox.Show("List signature count is different from list descriptor count", "Critical Error !", MessageBoxButtons.OK, MessageBoxIcon.Error);
cGlobalInfo.CurrentScreening.ListDescriptors.UpDateDisplay();
// CompleteScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < cGlobalInfo.CurrentScreening.ListPlatesAvailable.Count; idxP++)
cGlobalInfo.CurrentScreening.ListPlatesActive[idxP].UpDataMinMax();
StartingUpDateUI();
this.toolStripcomboBoxPlateList.Items.Clear();
for (int IdxPlate = 0; IdxPlate < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; IdxPlate++)
{
string Name = cGlobalInfo.CurrentScreening.ListPlatesActive.GetPlate(IdxPlate).GetName();
this.toolStripcomboBoxPlateList.Items.Add(Name);
PlateListWindow.listBoxPlateNameToProcess.Items.Add(Name);
PlateListWindow.listBoxAvaliableListPlates.Items.Add(Name);
}
cGlobalInfo.CurrentScreening.CurrentDisplayPlateIdx = 0;
cGlobalInfo.CurrentScreening.SetSelectionType(comboBoxClass.SelectedIndex - 1);
UpdateUIAfterLoading();
cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().DisplayDistribution(cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptor(), false);
}
private void mahalanobisDistanceToolStripMenuItem_Click(object sender, EventArgs e)
{
FormForMahalanobisDistance MainWindow = new FormForMahalanobisDistance();
PanelForClassSelection ClassSelectionPanel = new PanelForClassSelection(true, eClassType.WELL);
ClassSelectionPanel.Height = MainWindow.panelForSourceCloud.Height;
MainWindow.panelForSourceCloud.Controls.Add(ClassSelectionPanel);
PanelForClassSelection HitClassSelectionPanel = new PanelForClassSelection(false, eClassType.WELL);
HitClassSelectionPanel.Height = MainWindow.panelHitClass.Height;
HitClassSelectionPanel.ListRadioButtons[1].Checked = true;
MainWindow.panelHitClass.Controls.Add(HitClassSelectionPanel);
if (MainWindow.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
cExtendedList ListClassSelected = new cExtendedList();
for (int i = 0; i < ClassSelectionPanel.ListCheckBoxes.Count; i++)
if (ClassSelectionPanel.ListCheckBoxes[i].Checked) ListClassSelected.Add(1);
else
ListClassSelected.Add(0);
int IdxClassForOutliers = 0;
for (int i = 0; i < HitClassSelectionPanel.ListRadioButtons.Count; i++)
if (HitClassSelectionPanel.ListRadioButtons[i].Checked)
{
IdxClassForOutliers = i;
break;
}
if (ListClassSelected.Sum() < 1)
{
MessageBox.Show("At least one classe has to be selected.", "Error !", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
// start by computing the inversed covariance matrix
//if (checkedListBoxActiveDescriptors.CheckedItems.Count <= 1)
//{
// MessageBox.Show("At least two descriptors have to be selected", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
// return;
//}
cCovarianceMatrix CM = new cCovarianceMatrix();
cExtendedTable NewTable = null;
if (this.ProcessModeplateByPlateToolStripMenuItem.Checked)
{
//foreach (cPlate TmpPlate in CompleteScreening.ListPlatesActive)
//{
// cListWells ListWellsToProcess = new cListWells(null);
// foreach (cWell item in TmpPlate.ListActiveWells)
// if ((item.GetClassIdx() != -1) && (ListClassSelected[item.GetClassIdx()] == 1)) ListWellsToProcess.Add(item);
// cExtendedTable NewTable = new cExtendedTable(ListWellsToProcess, true);
// CM.SetInputData(NewTable);
//}
}
else if (this.ProcessModeEntireScreeningToolStripMenuItem.Checked)
{
cListWells ListWellsToProcess = new cListWells(null);
foreach (cPlate TmpPlate in cGlobalInfo.CurrentScreening.ListPlatesActive)
foreach (cWell item in TmpPlate.ListActiveWells)
if ((item.GetCurrentClassIdx() != -1) && (ListClassSelected[item.GetCurrentClassIdx()] == 1)) ListWellsToProcess.Add(item);
NewTable = new cExtendedTable(ListWellsToProcess, true);
// cTwoSampleFTest CM = new cTwoSampleFTest();
CM.SetInputData(NewTable);
}
else
{
cListWells ListWellsToProcess = new cListWells(null);
foreach (cWell item in cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().ListActiveWells)
if ((item.GetCurrentClassIdx() != -1) && (ListClassSelected[item.GetCurrentClassIdx()] == 1)) ListWellsToProcess.Add(item);
NewTable = new cExtendedTable(ListWellsToProcess, true);
// cTwoSampleFTest CM = new cTwoSampleFTest();
CM.SetInputData(NewTable);
}
CM.Run();
cInverse cI = new cInverse();
cI.SetInputData(CM.GetOutPut());
cI.Run();
// get the cloud center
cStatistics cstat = new cStatistics();
cstat.UnselectAll();
cstat.IsMean = true;
cstat.SetInputData(NewTable);
cstat.Run();
if (cstat.GetOutPut() == null) return;
cExtendedList ListMeans = cstat.GetOutPut().GetRow(0);
cDescriptorType MahalanobisType = new cDescriptorType("Mahalanobis Distance", true, 1);
#region Compute the Threshold
int DegreeOfFreedom = cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptors().Count;
cExtendedTable T = new cExtendedTable();
T.Add(new cExtendedList());
T[0].Add((double)MainWindow.numericUpDownPValue.Value);
cFunctions F = new cFunctions();
F.SetInputData(T);
F.IsInverse = true;
F.DegreeOfFreedom = DegreeOfFreedom;
F.Run();
double ThresholdForMahalanobis = Math.Sqrt(F.GetOutPut()[1][0]);
#endregion
int IdxClassForNonOutliers = 1;
foreach (cPlate TmpPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
for (int Col = 0; Col < cGlobalInfo.CurrentScreening.Columns; Col++)
for (int Row = 0; Row < cGlobalInfo.CurrentScreening.Rows; Row++)
{
cWell TmpWell = TmpPlate.GetWell(Col, Row, false);
if (TmpWell == null) continue;
double ValueDistance = TmpWell.GetAverageValuesList(true)[0].Dist_Mahalanobis(ListMeans, cI.GetOutPut());
if (ValueDistance > ThresholdForMahalanobis || double.IsNaN(ValueDistance) ) // that's an outlier
{
TmpWell.SetClass(IdxClassForOutliers);
}
else
{
TmpWell.SetClass(IdxClassForNonOutliers);
}
if (MainWindow.checkBoxDistAsDesc.Checked)
{
cListSignature LDesc = new cListSignature();
cSignature NewDesc = new cSignature(ValueDistance, MahalanobisType, cGlobalInfo.CurrentScreening);
LDesc.Add(NewDesc);
TmpWell.AddSignatures(LDesc);
}
}
}
if (MainWindow.checkBoxDistAsDesc.Checked)
{
cGlobalInfo.CurrentScreening.ListDescriptors.AddNew(MahalanobisType);
}
cGlobalInfo.CurrentScreening.ListDescriptors.UpDateDisplay();
cGlobalInfo.CurrentScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; idxP++)
cGlobalInfo.CurrentScreening.ListPlatesActive[idxP].UpDataMinMax();
}
private void SingleCellOperationsToDescriptorItem(object sender, EventArgs e)
{
List<string> ListNamesDesc = new List<string>();
foreach (var item in cGlobalInfo.CurrentScreening.ListDescriptors)
{
if (item.GetDataType() != "Single")
{
ListNamesDesc.Add(item.GetName());
}
}
FormForDescOperations MainWindow = new FormForDescOperations(ListNamesDesc);
if (MainWindow.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
string NewDescName = MainWindow.textBoxNewDescName.Text;
cDescriptorType DescType1 = cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorByName(MainWindow.comboBoxDescriptor1.Text);
cDescriptorType DescType2 = cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorByName(MainWindow.comboBoxDescriptor2.Text);
if ((DescType1 == null) || (DescType2 == null)) return;
FormForProgress ProgressWindow = new FormForProgress();
ProgressWindow.Show();
int IdxProgress = 1;
int MaxProgress = cGlobalInfo.CurrentScreening.ListPlatesAvailable.Count;
ProgressWindow.progressBar.Maximum = MaxProgress;
cDescriptorType NewDescType = new cDescriptorType(NewDescName, true, 256, true);
cGlobalInfo.CurrentScreening.ListDescriptors.AddNew(NewDescType);
//HCSAnalyzer.Classes.General_Types.cDBConnection.cSingleCellOperations SCO = new HCSAnalyzer.Classes.General_Types.cDBConnection.cSingleCellOperations()
cSingleCellOperations SingleCellOperation = new cSingleCellOperations();
if (MainWindow.tabControlMain.SelectedTab.Name == "tabPageBinary")
{
SingleCellOperation.ListDualOperations = new List<eBinaryOperationType>();
// eDualOperationType OperationType = eDualOperationType.ADD;
switch (MainWindow.domainUpDown1.Text)
{
case "*":
SingleCellOperation.ListDualOperations.Add(eBinaryOperationType.MULTIPLY);
break;
case "+":
SingleCellOperation.ListDualOperations.Add(eBinaryOperationType.ADD);
break;
case "/":
SingleCellOperation.ListDualOperations.Add(eBinaryOperationType.DIVIDE);
break;
case "-":
SingleCellOperation.ListDualOperations.Add(eBinaryOperationType.SUBSTRACT);
break;
default:
return;
}
if (MainWindow.checkBoxActivePostProcess.Checked)
{
SingleCellOperation.PostProcessingOperation = new List<eBinaryOperationType>();
switch (MainWindow.domainUpDownPostProcessOperator.Text)
{
case "*":
SingleCellOperation.PostProcessingOperation.Add(eBinaryOperationType.MULTIPLY);
break;
case "+":
SingleCellOperation.PostProcessingOperation.Add(eBinaryOperationType.ADD);
break;
case "/":
SingleCellOperation.PostProcessingOperation.Add(eBinaryOperationType.DIVIDE);
break;
case "-":
SingleCellOperation.PostProcessingOperation.Add(eBinaryOperationType.SUBSTRACT);
break;
default:
return;
}
SingleCellOperation.PostProcessingValue = (double)MainWindow.numericUpDownPostProcessValue.Value;
}
foreach (cPlate CurrentPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
CurrentPlate.DBConnection.OpenConnection();
CurrentPlate.DBConnection.CreateNewColumn(NewDescType,
DescType1,
DescType2,
SingleCellOperation,
GlobalInfo, ref CurrentPlate.ListActiveWells);
CurrentPlate.DBConnection.CloseConnection();
ProgressWindow.progressBar.Value = IdxProgress++;
ProgressWindow.richTextBoxForComment.AppendText(CurrentPlate.GetShortInfo());
ProgressWindow.Refresh();
}
}
else
{
eUnaryOperationType OperationType = eUnaryOperationType.LOG;
if (MainWindow.radioButtonSQRT.Checked)
OperationType = eUnaryOperationType.SQRT;
else if (MainWindow.radioButtonLog.Checked)
OperationType = eUnaryOperationType.LOG;
else if (MainWindow.radioButtonABS.Checked)
OperationType = eUnaryOperationType.ABS;
else if (MainWindow.radioButtonEXP.Checked)
OperationType = eUnaryOperationType.EXP;
foreach (cPlate CurrentPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
CurrentPlate.DBConnection.OpenConnection();
CurrentPlate.DBConnection.CreateNewColumn(NewDescType,
DescType1,
OperationType,
GlobalInfo, ref CurrentPlate.ListActiveWells);
CurrentPlate.DBConnection.CloseConnection();
ProgressWindow.progressBar.Value = IdxProgress++;
ProgressWindow.richTextBoxForComment.AppendText(CurrentPlate.GetShortInfo());
ProgressWindow.Refresh();
}
}
ProgressWindow.Close();
int IdxNull = 0;
foreach (cPlate TmpPlate in cGlobalInfo.CurrentScreening.ListPlatesActive)
{
foreach (cWell TmpWell in TmpPlate.ListActiveWells)
if (TmpWell.ListSignatures.Count != cGlobalInfo.CurrentScreening.ListDescriptors.Count)
IdxNull++;
}
if (IdxNull > 0)
System.Windows.Forms.MessageBox.Show("List signature count is different from list descriptor count", "Critical Error !", MessageBoxButtons.OK, MessageBoxIcon.Error);
cGlobalInfo.CurrentScreening.ListDescriptors.UpDateDisplay();
// CompleteScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < cGlobalInfo.CurrentScreening.ListPlatesAvailable.Count; idxP++)
cGlobalInfo.CurrentScreening.ListPlatesActive[idxP].UpDataMinMax();
StartingUpDateUI();
this.toolStripcomboBoxPlateList.Items.Clear();
for (int IdxPlate = 0; IdxPlate < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; IdxPlate++)
{
string Name = cGlobalInfo.CurrentScreening.ListPlatesActive.GetPlate(IdxPlate).GetName();
this.toolStripcomboBoxPlateList.Items.Add(Name);
PlateListWindow.listBoxPlateNameToProcess.Items.Add(Name);
PlateListWindow.listBoxAvaliableListPlates.Items.Add(Name);
}
cGlobalInfo.CurrentScreening.CurrentDisplayPlateIdx = 0;
cGlobalInfo.CurrentScreening.SetSelectionType(comboBoxClass.SelectedIndex - 1);
UpdateUIAfterLoading();
cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().DisplayDistribution(cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptor(), false);
}
private void SumCheckedDescToDescriptorItem(object sender, EventArgs e)
{
string NewName = "";
string Description = "Sum of:\n";
for (int Idx = 0; Idx < cGlobalInfo.WindowHCSAnalyzer.checkedListBoxActiveDescriptors.Items.Count; Idx++)
{
if (cGlobalInfo.CurrentScreening.ListDescriptors[Idx].IsActive())
if (cGlobalInfo.CurrentScreening.ListDescriptors[Idx].GetBinNumber() == 1)
{
NewName += cGlobalInfo.CurrentScreening.ListDescriptors[Idx].GetName() + "+";
Description += cGlobalInfo.CurrentScreening.ListDescriptors[Idx].GetName() + "+\n";
}
else
{
MessageBox.Show("Descriptor length not consistent (" + cGlobalInfo.CurrentScreening.ListDescriptors[Idx].GetName() + " : " + cGlobalInfo.CurrentScreening.ListDescriptors[Idx].GetBinNumber() + " bins", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
}
cDescriptorType ColumnType = new cDescriptorType(NewName.Remove(NewName.Length - 1), true, 1);
ColumnType.description = Description;
cGlobalInfo.CurrentScreening.ListDescriptors.AddNew(ColumnType);
foreach (cPlate TmpPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
foreach (cWell Tmpwell in TmpPlate.ListActiveWells)
{
cListSignature LDesc = new cListSignature();
double NewValue = 0;
for (int IdxActiveDesc = 0; IdxActiveDesc < cGlobalInfo.CurrentScreening.ListDescriptors.Count - 1; IdxActiveDesc++)
{
if (cGlobalInfo.CurrentScreening.ListDescriptors[IdxActiveDesc].IsActive())
NewValue += Tmpwell.ListSignatures[IdxActiveDesc].GetValue();
}
cSignature NewDesc = new cSignature(NewValue, ColumnType, cGlobalInfo.CurrentScreening);
LDesc.Add(NewDesc);
Tmpwell.AddSignatures(LDesc);
}
}
cGlobalInfo.CurrentScreening.ListDescriptors.UpDateDisplay();
cGlobalInfo.CurrentScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; idxP++)
cGlobalInfo.CurrentScreening.ListPlatesActive[idxP].UpDataMinMax();
}
public cExtendedTable GetAverageValueTable(cDescriptorType DescriptorType, bool OnlySelectedWells)
{
cExtendedTable DV = new cExtendedTable(ParentScreening.Columns, ParentScreening.Rows, double.NaN);
DV.ListRowNames = new List<string>();
for (int i = 0; i < ParentScreening.Columns; i++)
{
DV[i].Name = (i + 1).ToString();
DV[i].ListTags = new List<object>();
for (int j = 0; j < ParentScreening.Rows; j++)
{
if (i == 0)
{
byte[] strArray = new byte[1];
strArray[0] = (byte)(j + 65);
string Chara = Encoding.UTF7.GetString(strArray);
DV.ListRowNames.Add(String.Format("{0}\t", Chara));
}
cWell TmpWell = this.GetWell(i, j, OnlySelectedWells);
if (TmpWell != null)
{
DV[i].ListTags.Add(TmpWell);
DV[i][j] = TmpWell.GetAverageValue(DescriptorType);
}
}
}
DV.Name = this.GetName() + " - " + DescriptorType.GetName();
return DV;
}
public cExtendedTable GetMinMax(cDescriptorType DescriptorType)
{
cExtendedList MinMax = new cExtendedList();
MinMax.Name = "Min-Max";
cExtendedTable ListValues = this.GetAverageValueList(DescriptorType, false);
if (ListValues == null) return null;
MinMax.Add(ListValues.Min());
MinMax.Add(ListValues.Max());
return new cExtendedTable(MinMax);
}
public double GetAverageValue(cDescriptorType DescriptorType)
{
return ListSignatures.GetSignature(DescriptorType).GetValue();
}
public cExtendedTable GetAverageValueList(cDescriptorType DescriptorType, bool OnlySelectedWells)
{
List<cDescriptorType> LDesc = new List<cDescriptorType>();
LDesc.Add(DescriptorType);
cExtendedTable DV = this.ListActiveWells.GetAverageDescriptorValues(LDesc, false, false);
return DV;
}
public cViewerStackedHistogram GetViewerStackedHistogram(cDescriptorType DT)
{
cListWells LW = new cListWells(this);
return LW.GetSingleCellStackedHisto(DT,null);
}
public cExtendedTable GetValuesList(cDescriptorType DescriptorType)
{
this.AssociatedPlate.DBConnection = new cDBConnection(this.AssociatedPlate, this.SQLTableName);
cListSingleBiologicalObjects ListPhenotypes =
this.AssociatedPlate.DBConnection.GetBiologicalPhenotypes(this);
cExtendedTable ET = this.AssociatedPlate.DBConnection.GetWellValues(this, DescriptorType);
this.AssociatedPlate.DBConnection.CloseConnection();
return ET;
}
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 (cGlobalInfo.CurrentScreening != null) cGlobalInfo.CurrentScreening.Close3DView();
// CompleteScreening.ListDescriptors.RemoveDesc(CompleteScreening.ListDescriptors[IntToTransfer], CompleteScreening);
cScreening MergedScreening = new cScreening("Merged Screen");
MergedScreening.PanelForPlate = this.panelForPlate;
MergedScreening.Rows = cGlobalInfo.CurrentScreening.Rows;
MergedScreening.Columns = cGlobalInfo.CurrentScreening.Columns;
MergedScreening.ListPlatesAvailable = new cListPlates(null);
// create the descriptor
MergedScreening.ListDescriptors.Clean();
int Idesc = 0;
List<cDescriptorType> ListDescType = new List<cDescriptorType>();
for (int i = 0; i < cGlobalInfo.CurrentScreening.ListDescriptors.Count; i++)
{
if (!cGlobalInfo.CurrentScreening.ListDescriptors[i].IsActive()) continue;
cDescriptorType DescEC50 = new cDescriptorType("EC50_" + cGlobalInfo.CurrentScreening.ListDescriptors[i].GetName(), true, 1);
ListDescType.Add(DescEC50);
MergedScreening.ListDescriptors.AddNew(DescEC50);
cDescriptorType DescTop = new cDescriptorType("Top_" + cGlobalInfo.CurrentScreening.ListDescriptors[i].GetName(), true, 1);
ListDescType.Add(DescTop);
MergedScreening.ListDescriptors.AddNew(DescTop);
cDescriptorType DescBottom = new cDescriptorType("Bottom_" + cGlobalInfo.CurrentScreening.ListDescriptors[i].GetName(), true, 1);
ListDescType.Add(DescBottom);
MergedScreening.ListDescriptors.AddNew(DescBottom);
cDescriptorType DescSlope = new cDescriptorType("Slope_" + cGlobalInfo.CurrentScreening.ListDescriptors[i].GetName(), true, 1);
ListDescType.Add(DescSlope);
MergedScreening.ListDescriptors.AddNew(DescSlope);
Idesc++;
}
MergedScreening.ListDescriptors.CurrentSelectedDescriptorIdx = 0;
foreach (cPlate CurrentPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
cPlate NewPlate = new cPlate(CurrentPlate.GetName() + " Merged", MergedScreening);
// check if the plate exist already
MergedScreening.AddPlate(NewPlate);
foreach (cDRC_Region CurrentRegion in CurrentPlate.ListDRCRegions)
{
cListSignature LDesc = new cListSignature();
Idesc = 0;
int IDESCBase = 0;
for (int i = 0; i < cGlobalInfo.CurrentScreening.ListDescriptors.Count; i++)
{
if (!cGlobalInfo.CurrentScreening.ListDescriptors[i].IsActive()) continue;
cDRC CurrentDRC = CurrentRegion.GetDRC(cGlobalInfo.CurrentScreening.ListDescriptors[IDESCBase++]);
cSignature Desc_EC50 = new cSignature(CurrentDRC.EC50, ListDescType[Idesc++], cGlobalInfo.CurrentScreening);
LDesc.Add(Desc_EC50);
cSignature Desc_Top = new cSignature(CurrentDRC.Top, ListDescType[Idesc++], cGlobalInfo.CurrentScreening);
LDesc.Add(Desc_Top);
cSignature Desc_Bottom = new cSignature(CurrentDRC.Bottom, ListDescType[Idesc++], cGlobalInfo.CurrentScreening);
LDesc.Add(Desc_Bottom);
cSignature Desc_Slope = new cSignature(CurrentDRC.Slope, ListDescType[Idesc++], cGlobalInfo.CurrentScreening);
LDesc.Add(Desc_Slope);
}
cWell NewWell = new cWell(LDesc, CurrentRegion.PosXMin + 1, CurrentRegion.PosYMin + 1, MergedScreening, NewPlate);
NewWell.ListProperties.UpdateValueByName("Compound Name","DRC [" + CurrentRegion.PosXMin + ":" + CurrentRegion.PosYMin + "]");
NewPlate.AddWell(NewWell);
}
}
// PanelList[0].CurrentScreening.ListPlatesActive.Clear();
// PanelList[0].CurrentScreening.GlobalInfo.WindowHCSAnalyzer.RefreshInfoScreeningRichBox();
MergedScreening.ListPlatesActive = new cListPlates();
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);
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.GetCurrentDisplayPlate().DisplayDistribution(cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptor(), true);
}
private void RowToDescriptorItem(object sender, EventArgs e)
{
cDescriptorType RowType = new cDescriptorType("Row", true, 1);
cGlobalInfo.CurrentScreening.ListDescriptors.AddNew(RowType);
foreach (cPlate TmpPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
foreach (cWell Tmpwell in TmpPlate.ListActiveWells)
{
cListSignature LDesc = new cListSignature();
cSignature NewDesc = new cSignature(Tmpwell.GetPosY(), RowType, cGlobalInfo.CurrentScreening);
LDesc.Add(NewDesc);
Tmpwell.AddSignatures(LDesc);
}
}
cGlobalInfo.CurrentScreening.ListDescriptors.UpDateDisplay();
cGlobalInfo.CurrentScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; idxP++)
cGlobalInfo.CurrentScreening.ListPlatesActive[idxP].UpDataMinMax();
}
public void ComputePlateBasedDescriptors()
{
cDescriptorType TypeRow = new cDescriptorType("Row_Pos", true, 1);
cDescriptorType TypeCol = new cDescriptorType("Col_Pos", true, 1);
cDescriptorType TypeDistBorder = new cDescriptorType("Dist_To_Border", true, 1);
cDescriptorType TypeDistCenter = new cDescriptorType("Dist_To_Center", true, 1);
for (int j = 0; j < ParentScreening.Rows; j++)
for (int i = 0; i < ParentScreening.Columns; i++)
{
cWell TempWell = GetWell(i, j, false);
if (TempWell == null) continue;
TempWell.ListPlateBasedDescriptors = new cListSignature();
cSignature Descriptor0 = new cSignature(j, TypeRow, this.ParentScreening);
TempWell.ListPlateBasedDescriptors.Add(Descriptor0);
cSignature Descriptor1 = new cSignature(i, TypeCol, this.ParentScreening);
TempWell.ListPlateBasedDescriptors.Add(Descriptor1);
double MinDist = i + 1;
double DistToRight = ParentScreening.Columns - i;
if (DistToRight < MinDist) MinDist = DistToRight;
double DistToTop = j + 1;
if (DistToTop < MinDist) MinDist = DistToTop;
double DistToBottom = ParentScreening.Rows - j;
if (DistToBottom < MinDist) MinDist = DistToBottom;
cSignature Descriptor2 = new cSignature(MinDist, TypeDistBorder, this.ParentScreening);
TempWell.ListPlateBasedDescriptors.Add(Descriptor2);
double X_Center = ParentScreening.Columns / 2;
double Y_Center = ParentScreening.Rows / 2;
double DistToCenter = Math.Sqrt((i - X_Center) * (i - X_Center) + (j - Y_Center) * (j - Y_Center));
cSignature Descriptor3 = new cSignature(DistToCenter, TypeDistCenter, this.ParentScreening);
TempWell.ListPlateBasedDescriptors.Add(Descriptor3);
}
return;
}
private void SingleCellOperationPhenotypToDesc(object sender, EventArgs e)
{
string description = "This descriptor has been generated by converting single cell phenotypic class into feature\n";
FormForNameRequest FFNR = new FormForNameRequest();
FFNR.Text = "Descriptor Name";
FFNR.textBoxForName.Text = "Phenotype Class";
if (FFNR.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
if (FFNR.textBoxForName.Text == "") return;
cDescriptorType NewDescType = new cDescriptorType(FFNR.textBoxForName.Text, true, cGlobalInfo.ListCellularPhenotypes.Count, true);
cGlobalInfo.CurrentScreening.ListDescriptors.AddNew(NewDescType);
FormForProgress ProgressWindow = new FormForProgress();
ProgressWindow.Show();
int IdxProgress = 0;
int MaxProgress = 0;
foreach (cPlate CurrentPlateToProcess in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
MaxProgress += (int)CurrentPlateToProcess.ListActiveWells.Count;
ProgressWindow.progressBar.Maximum = MaxProgress;
foreach (cPlate CurrentPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
CurrentPlate.DBConnection.OpenConnection();
CurrentPlate.DBConnection.CreateNewColumnFromExisting(NewDescType, "Phenotype_Class", GlobalInfo, ref CurrentPlate.ListActiveWells);
CurrentPlate.DBConnection.CloseConnection();
ProgressWindow.progressBar.Value = IdxProgress++;
ProgressWindow.progressBar.Refresh();
}
ProgressWindow.Close();
int IdxNull = 0;
foreach (cPlate TmpPlate in cGlobalInfo.CurrentScreening.ListPlatesActive)
{
foreach (cWell TmpWell in TmpPlate.ListActiveWells)
if (TmpWell.ListSignatures.Count != cGlobalInfo.CurrentScreening.ListDescriptors.Count)
IdxNull++;
}
if (IdxNull > 0)
System.Windows.Forms.MessageBox.Show("List signature count is different from list descriptor count", "Critical Error !", MessageBoxButtons.OK, MessageBoxIcon.Error);
cGlobalInfo.CurrentScreening.ListDescriptors.UpDateDisplay();
// CompleteScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < cGlobalInfo.CurrentScreening.ListPlatesAvailable.Count; idxP++)
cGlobalInfo.CurrentScreening.ListPlatesActive[idxP].UpDataMinMax();
StartingUpDateUI();
this.toolStripcomboBoxPlateList.Items.Clear();
for (int IdxPlate = 0; IdxPlate < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; IdxPlate++)
{
string Name = cGlobalInfo.CurrentScreening.ListPlatesActive.GetPlate(IdxPlate).GetName();
this.toolStripcomboBoxPlateList.Items.Add(Name);
PlateListWindow.listBoxPlateNameToProcess.Items.Add(Name);
PlateListWindow.listBoxAvaliableListPlates.Items.Add(Name);
}
cGlobalInfo.CurrentScreening.CurrentDisplayPlateIdx = 0;
cGlobalInfo.CurrentScreening.SetSelectionType(comboBoxClass.SelectedIndex - 1);
UpdateUIAfterLoading();
cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().DisplayDistribution(cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptor(), false);
}
public void DisplayDistribution(cDescriptorType Descriptor, bool IsFirstTime, object Sender = null)
{
this.DisplayDistribution(ParentScreening.ListDescriptors.GetDescriptorIndex(Descriptor), IsFirstTime, Sender);
}
private void SubPopulationStatDescItem(object sender, EventArgs e)
{
PanelForClassSelection ClassSelectionPanel = new PanelForClassSelection(true, eClassType.PHENOTYPE);
//ClassSelectionPanel.Height = WindowToDisplay.Height;
ClassSelectionPanel.UnSelectAll();
ClassSelectionPanel.Select(0);
ClassSelectionPanel.Select(1);
ClassSelectionPanel.Location = new System.Drawing.Point(10, 10);
ClassSelectionPanel.Width = 150;
ClassSelectionPanel.Height = ClassSelectionPanel.ListCheckBoxes.Count * 25;
ClassSelectionPanel.BorderStyle = BorderStyle.Fixed3D;
FormForStatDesc NewWindow = new FormForStatDesc(this.GlobalInfo);
NewWindow.panelForSubPopulation.Controls.Add(ClassSelectionPanel);
NewWindow.textBoxDescName.Text = cGlobalInfo.CurrentScreening.ListDescriptors[IntToTransfer].GetName() + "_Average";
if (NewWindow.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
if ((NewWindow.comboBoxStatistics.Text != "Average") && (NewWindow.comboBoxStatistics.Text != "Stdev") &&
(NewWindow.comboBoxStatistics.Text != "Sum") && (NewWindow.comboBoxStatistics.Text != "Median") && (NewWindow.comboBoxStatistics.Text != "MAD") && (NewWindow.comboBoxStatistics.Text != "CV%"))
return;
List<cCellularPhenotype> LCP = new List<cCellularPhenotype>();
for (int IdxPheno = 0; IdxPheno < ClassSelectionPanel.GetListSelectedClass().Count; IdxPheno++)
{
if (ClassSelectionPanel.GetListSelectedClass()[IdxPheno])
LCP.Add(cGlobalInfo.ListCellularPhenotypes[IdxPheno]);
}
if (LCP.Count == 0) return;
double RatioPopulation = 1;
string description = "This descriptor has been generated by computing the " + NewWindow.textBoxDescName.Text + " of " + RatioPopulation * 100 + "% the following phenotypic sub-populations:\n";
foreach (var item in LCP)
{
description += item.Name + "\n";
}
cDescriptorType NewAverageType = new cDescriptorType(NewWindow.textBoxDescName.Text, true, 1, description);
cGlobalInfo.CurrentScreening.ListDescriptors.AddNew(NewAverageType);
FormForProgress ProgressWindow = new FormForProgress();
ProgressWindow.Show();
int IdxProgress = 0;
int MaxProgress = 0;
foreach (cPlate CurrentPlateToProcess in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
MaxProgress += (int)CurrentPlateToProcess.ListActiveWells.Count;
ProgressWindow.progressBar.Maximum = MaxProgress;
foreach (cPlate TmpPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
foreach (cWell Tmpwell in TmpPlate.ListActiveWells)
{
TmpPlate.DBConnection = new cDBConnection(TmpPlate, Tmpwell.SQLTableName);
List<cDescriptorType> LDT = new List<cDescriptorType>();
LDT.Add(cGlobalInfo.CurrentScreening.ListDescriptors[IntToTransfer]);
cExtendedTable CT = TmpPlate.DBConnection.GetWellValues(Tmpwell, LDT, LCP, RatioPopulation);
cListSignature LDesc = new cListSignature();
double Value = 0;
if (CT.Count == 1)
{
if (CT[0].Count == 0)
{
Value = 0;
richTextBoxConsole.AppendText(TmpPlate.GetName() + " : " + Tmpwell.GetShortInfo().Remove(Tmpwell.GetShortInfo().Length - 2) + ": no objects fullfill your request. Statistics set to null.\n");
}
else
{
if (NewWindow.comboBoxStatistics.Text == "Average")
Value = CT[0].Average();
else if (NewWindow.comboBoxStatistics.Text == "Stdev")
Value = CT[0].Std();
else if (NewWindow.comboBoxStatistics.Text == "Sum")
Value = CT[0].Sum();
else if (NewWindow.comboBoxStatistics.Text == "Median")
Value = CT[0].Median();
else if (NewWindow.comboBoxStatistics.Text == "MAD")
Value = CT[0].MAD(true);
else if (NewWindow.comboBoxStatistics.Text == "CV%")
Value = CT[0].CV();
}
}
ProgressWindow.richTextBoxForComment.AppendText(Tmpwell.GetShortInfo() + ": " + CT[0].Count.ToString() + " / " + Tmpwell.GetNumBiologicalObjects() + "\n");
cSignature NewDesc = new cSignature(Value, NewAverageType, cGlobalInfo.CurrentScreening);
LDesc.Add(NewDesc);
Tmpwell.AddSignatures(LDesc);
TmpPlate.DBConnection.CloseConnection();
ProgressWindow.progressBar.Value = IdxProgress++;
ProgressWindow.richTextBoxForComment.AppendText(TmpPlate.GetName() + " : " + Tmpwell.GetShortInfo().Remove(Tmpwell.GetShortInfo().Length - 2) + "\n");
ProgressWindow.Refresh();
}
}
ProgressWindow.Close();
cGlobalInfo.CurrentScreening.ListDescriptors.UpDateDisplay();
cGlobalInfo.CurrentScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; idxP++)
cGlobalInfo.CurrentScreening.ListPlatesActive[idxP].UpDataMinMax();
}
public void ExportToHTML(cDescriptorType Desc)
{
if (Desc.IsConnectedToDatabase == false) return;
List<cDescriptorType> LCDT = new List<cDescriptorType>();
LCDT.Add(Desc);
List<cCellularPhenotype> ListCellularPhenotypesToBeSelected = new List<cCellularPhenotype>();
cGUI_ListClasses GUIClasses = new cGUI_ListClasses();
GUIClasses.IsCheckBoxes = true;
GUIClasses.IsSelectAll = true;
GUIClasses.ClassType = eClassType.PHENOTYPE;
if (!GUIClasses.Run().IsSucceed) return;
int IDx = 0;
foreach (var item in cGlobalInfo.ListCellularPhenotypes)
{
if ((GUIClasses.GetOutPut()[0][IDx++] != 0))
ListCellularPhenotypesToBeSelected.Add(item);
}
cExtendedTable ET = new cExtendedTable(cGlobalInfo.CurrentScreening.Columns, cGlobalInfo.CurrentScreening.Rows, 0);
ET.Name = this.Name + " [" + Desc.GetName() + "]";
ET.ListRowNames = new List<string>();
for (int i = 0; i < ET[0].Count; i++)
{
ET.ListRowNames.Add(((char)(i + 65)).ToString());
}
FormForProgress MyProgressBar = new FormForProgress();
MyProgressBar.progressBar.Maximum = this.ListActiveWells.Count;
MyProgressBar.Show();
//ET.ListTags = new List<object>();
for (int i = 0; i < cGlobalInfo.CurrentScreening.Columns; i++)
{
ET[i].ListTags = new List<object>();
ET[i].Name = (i + 1).ToString();
for (int j = 0; j < cGlobalInfo.CurrentScreening.Rows; j++)
{
MyProgressBar.progressBar.Update();
cWell TmpWell = this.GetWell(i, j, true);
if (TmpWell == null)
{
ET[i].ListTags.Add("n.a.");
continue;
}
MyProgressBar.progressBar.Value++;
cExtendedTable TmpET = null;
if (cGlobalInfo.OptionsWindow.FFAllOptions.checkBoxHTMLExportStackedHisto.Checked)
TmpET = TmpWell.GetValuesList(LCDT, ListCellularPhenotypesToBeSelected, true);
else
TmpET = TmpWell.GetValuesList(LCDT, ListCellularPhenotypesToBeSelected, false);
TmpET.Name = "[" + TmpWell.GetPos() + "] - " + TmpET[0].Count + " Objects";
// get the values associated to this well and descriptor
if (cGlobalInfo.OptionsWindow.FFAllOptions.checkBoxHTMLExportStackedHisto.Checked)
{
cExtendedTable FinalTable = new cExtendedTable();
FinalTable.Name = "Stacked Histogram - " + this.GetName();
int Idx = 0;
foreach (var item in cGlobalInfo.ListCellularPhenotypes)
{
FinalTable.Add(new cExtendedList());
FinalTable[Idx].Name = item.Name;
FinalTable[Idx].Tag = item;
for (int k = 0; k < TmpET[1].Count; k++)
{
if (TmpET[1][k] == Idx)
FinalTable[Idx].Add(TmpET[0][k]);
}
Idx++;
}
cViewerStackedHistogram VSH = new cViewerStackedHistogram();
VSH.SetInputData(FinalTable);//TmpET);
VSH.Chart.LabelAxisX = Desc.GetName();
VSH.Chart.IsLine = false;
VSH.Chart.CurrentTitle.Text = TmpET.Name;
if ((cGlobalInfo.OptionsWindow.radioButtonHistoDisplayManualMinMax.Checked) || (cGlobalInfo.OptionsWindow.radioButtonHistoDisplayAutomatedMinMax.Checked))
{
VSH.Chart.DefaultAxisXMin = new cExtendedList();
VSH.Chart.DefaultAxisXMin.Add((double)cGlobalInfo.OptionsWindow.numericUpDownManualMin.Value);
VSH.Chart.DefaultAxisXMax = new cExtendedList();
VSH.Chart.DefaultAxisXMax.Add((double)cGlobalInfo.OptionsWindow.numericUpDownManualMax.Value);
if (cGlobalInfo.OptionsWindow.FFAllOptions.checkBoxHTMLExportBackColorClass.Checked)
VSH.Chart.BackgroundColor = TmpWell.GetClassColor();
}
VSH.Chart.BinNumber = Desc.GetBinNumber();
VSH.Chart.IsShadow = false;
VSH.Chart.IsBorder = false;
VSH.Run();
ET[i].ListTags.Add((Chart)VSH.Chart);
}
else
{
cViewerHistogram VH = new cViewerHistogram();
VH.SetInputData(TmpET);
VH.Chart.LabelAxisX = Desc.GetName();
VH.Chart.CurrentTitle.Text = TmpET.Name;
if ((cGlobalInfo.OptionsWindow.radioButtonHistoDisplayManualMinMax.Checked) || (cGlobalInfo.OptionsWindow.radioButtonHistoDisplayAutomatedMinMax.Checked))
{
VH.Chart.DefaultAxisXMin = new cExtendedList();
VH.Chart.DefaultAxisXMin.Add((double)cGlobalInfo.OptionsWindow.numericUpDownManualMin.Value);
VH.Chart.DefaultAxisXMax = new cExtendedList();
VH.Chart.DefaultAxisXMax.Add((double)cGlobalInfo.OptionsWindow.numericUpDownManualMax.Value);
if (cGlobalInfo.OptionsWindow.FFAllOptions.checkBoxHTMLExportBackColorClass.Checked)
VH.Chart.BackgroundColor = TmpWell.GetClassColor();
}
VH.Run();
ET[i].ListTags.Add((Chart)VH.Chart);
}
}
}
MyProgressBar.Close();
cTableToHTML TToHTML = new cTableToHTML();
TToHTML.IsDisplayUIForFilePath = true;
TToHTML.SetInputData(ET);
TToHTML.Run();
}
private void AddCorrelatedSquareDescItem(object sender, EventArgs e)
{
cDescriptorType ColumnType = new cDescriptorType("Square(" + cGlobalInfo.CurrentScreening.ListDescriptors[IntToTransfer].GetName() + ")", true, 1);
cGlobalInfo.CurrentScreening.ListDescriptors.AddNew(ColumnType);
foreach (cPlate TmpPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
foreach (cWell Tmpwell in TmpPlate.ListActiveWells)
{
cListSignature LDesc = new cListSignature();
cSignature NewDesc = new cSignature(Math.Pow(Tmpwell.ListSignatures[IntToTransfer].GetValue(), 2), ColumnType, cGlobalInfo.CurrentScreening);
LDesc.Add(NewDesc);
Tmpwell.AddSignatures(LDesc);
}
}
cGlobalInfo.CurrentScreening.ListDescriptors.UpDateDisplay();
cGlobalInfo.CurrentScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; idxP++)
cGlobalInfo.CurrentScreening.ListPlatesActive[idxP].UpDataMinMax();
}
void ConvertItem_Click(object sender, EventArgs e)
{
if (sender.GetType() != typeof(ToolStripMenuItem)) return;
ToolStripMenuItem TMI = (ToolStripMenuItem)(sender);
cPropertyType CP = null;
if ((TMI.Tag != null) && (TMI.Tag.GetType() == typeof(cPropertyType)))
CP = (cPropertyType)(TMI.Tag);
else
return;
cDescriptorType ClassType = new cDescriptorType(CP.Name, true, 1);
cGlobalInfo.CurrentScreening.ListDescriptors.AddNew(ClassType);
foreach (cPlate TmpPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
foreach (cWell Tmpwell in TmpPlate.ListWells)
{
cListSignature LDesc = new cListSignature();
double TmpValue = 0;
object TmpObj = Tmpwell.ListProperties.FindByName(CP.Name).GetValue();
if ((TmpObj==null)||(!double.TryParse(TmpObj.ToString(), out TmpValue)))
TmpValue = 0;
cSignature NewDesc = new cSignature(TmpValue, ClassType, cGlobalInfo.CurrentScreening);
LDesc.Add(NewDesc);
Tmpwell.AddSignatures(LDesc);
}
}
cGlobalInfo.CurrentScreening.ListDescriptors.UpDateDisplay();
cGlobalInfo.CurrentScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; idxP++)
cGlobalInfo.CurrentScreening.ListPlatesActive[idxP].UpDataMinMax();
}
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();
}
public void CreateNewColumn(cDescriptorType NewDescType, cDescriptorType Desc0, eUnaryOperationType OperationType, cGlobalInfo GlobalInfo, ref cListWells ListWell)
{
string ColumnName = NewDescType.GetName();
int NumTableProcessed = 0;
foreach (var item in GetListTableNames()) // loop over the wells
{
// compute the new values
List<cDescriptorType> LDes = new List<cDescriptorType>();
LDes.Add(Desc0);
// LDes.Add(Desc1);
cExtendedTable LValues = this.GetWellValues(item, LDes);
cExtendedList ListResults = new cExtendedList();// LValues[0].Operation(LValues[1], OperationType);
if (OperationType == eUnaryOperationType.LOG)
{
for (int i = 0; i < LValues[0].Count; i++)
{
double tmpVal = LValues[0][i];
if (tmpVal <= 0) tmpVal = double.Epsilon;
ListResults.Add(Math.Log10(tmpVal));
}
}
else if (OperationType == eUnaryOperationType.SQRT)
{
for (int i = 0; i < LValues[0].Count; i++)
{
double tmpVal = LValues[0][i];
if (tmpVal < 0) tmpVal = 0;
ListResults.Add(Math.Sqrt(tmpVal));
}
}
else if (OperationType == eUnaryOperationType.ABS)
{
for (int i = 0; i < LValues[0].Count; i++)
{
double tmpVal = LValues[0][i];
ListResults.Add(Math.Abs(tmpVal));
}
}
else if (OperationType == eUnaryOperationType.EXP)
{
for (int i = 0; i < LValues[0].Count; i++)
{
double tmpVal = LValues[0][i];
ListResults.Add(Math.Exp(tmpVal));
}
}
#region Update the database
// create new column
SQLiteCommand mycommand = new SQLiteCommand(_SQLiteConnection);
String SQL = "ALTER TABLE \"" + item + "\" ADD COLUMN \"" + ColumnName + "\" REAL DEFAULT 0";
using (SQLiteCommand Command = new SQLiteCommand(SQL, _SQLiteConnection))
{
Command.ExecuteNonQuery();
}
// write data
using (SQLiteTransaction transaction = _SQLiteConnection.BeginTransaction())
using (SQLiteDataAdapter sqliteAdapter = new SQLiteDataAdapter("SELECT * FROM \"" + item + "\"", _SQLiteConnection))
{
DataSet DS = new DataSet();
sqliteAdapter.Fill(DS);
using (sqliteAdapter.InsertCommand = new SQLiteCommandBuilder(sqliteAdapter).GetUpdateCommand())
{
for (int i = 0; i < DS.Tables[0].Rows.Count; i++)
DS.Tables[0].Rows[i][ColumnName] = ListResults[i];
sqliteAdapter.Update(DS);
}
transaction.Commit();
}
#endregion
#region Update the screening data
cListSignature LDesc = new cListSignature();
cSignature NewSignature = new cSignature(ListResults, 256, NewDescType, cGlobalInfo.CurrentScreening);
LDesc.Add(NewSignature);
string[] Positions = item.Split('x');
ListWell.GetFirstWell(int.Parse(Positions[1]), int.Parse(Positions[2])).AddSignatures(LDesc);
#endregion
NumTableProcessed++;
}
}
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();
}
public void CreateNewColumnFromExisting(cDescriptorType NewDescType, string DescToBeDuplicated, cGlobalInfo GlobalInfo, ref cListWells ListWell)
{
this.CreateNewColumn(NewDescType.GetName(), 0);
// cExtendedList ListResults = null;
foreach (var item in GetListTableNames())
{
SQLiteCommand mycommand = new SQLiteCommand(_SQLiteConnection);
//update tableName set onefield = secondfield;
string SQL = "UPDATE \"" + item + "\" SET \"" + NewDescType.GetName() + "\" = \"" + DescToBeDuplicated + "\"";
using (SQLiteCommand Command = new SQLiteCommand(SQL, _SQLiteConnection))
{
Command.ExecuteNonQuery();
}
#region Update the screening data
List<cDescriptorType> LDes = new List<cDescriptorType>();
LDes.Add(NewDescType);
cExtendedTable LValues = this.GetWellValues(item, LDes);
cListSignature LDesc = new cListSignature();
cSignature NewSignature = new cSignature(LValues[0], NewDescType.GetBinNumber(), NewDescType, cGlobalInfo.CurrentScreening);
LDesc.Add(NewSignature);
string[] Positions = item.Split('x');
ListWell.GetFirstWell(int.Parse(Positions[1]), int.Parse(Positions[2])).AddSignatures(LDesc);
#endregion
}
return;
}
private void ConcentrationToDescriptorItem(object sender, EventArgs e)
{
cDescriptorType ConcentrationType = new cDescriptorType("Concentration", true, 1);
cGlobalInfo.CurrentScreening.ListDescriptors.AddNew(ConcentrationType);
foreach (cPlate TmpPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
foreach (cWell Tmpwell in TmpPlate.ListActiveWells)
{
cListSignature LDesc = new cListSignature();
object ConcentrationValue = Tmpwell.ListProperties.FindValueByName("Concentration");
float Value = 0;
if (ConcentrationValue == null)
{
Value = 0;
richTextBoxConsole.AppendText(Tmpwell.GetShortInfo() + ": Concentration NULL. Value set to 0\n");
}
else
Value = (float)ConcentrationValue;
cSignature NewDesc = new cSignature(Value, ConcentrationType, cGlobalInfo.CurrentScreening);
LDesc.Add(NewDesc);
Tmpwell.AddSignatures(LDesc);
}
}
cGlobalInfo.CurrentScreening.ListDescriptors.UpDateDisplay();
cGlobalInfo.CurrentScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; idxP++)
cGlobalInfo.CurrentScreening.ListPlatesActive[idxP].UpDataMinMax();
}
/// <summary>
/// Create a new column in the database of the current plate
/// </summary>
/// <param name="ColumnName">Column name</param>
/// <param name="DefaultValue">Array of values</param>
/// <returns>Return the number of table (i.e. wells) processed</returns>
public void CreateNewColumn(cDescriptorType NewDescType, cDescriptorType Desc0, cDescriptorType Desc1,
cSingleCellOperations SingleCellOperations,
cGlobalInfo GlobalInfo, ref cListWells ListWell)
{
string ColumnName = NewDescType.GetName();
int NumTableProcessed = 0;
foreach (var item in GetListTableNames()) // loop over the wells
{
// compute the new values
List<cDescriptorType> LDes = new List<cDescriptorType>();
LDes.Add(Desc0);
LDes.Add(Desc1);
cExtendedTable LValues = this.GetWellValues(item, LDes);
cExtendedList ListResults = LValues[0].Operation(LValues[1], SingleCellOperations.ListDualOperations[0]);
if ((SingleCellOperations.PostProcessingOperation != null) && (SingleCellOperations.PostProcessingOperation.Count > 0))
{
switch (SingleCellOperations.PostProcessingOperation[0])
{
case eBinaryOperationType.ADD:
ListResults += SingleCellOperations.PostProcessingValue;
break;
case eBinaryOperationType.SUBSTRACT:
ListResults -= SingleCellOperations.PostProcessingValue;
break;
case eBinaryOperationType.MULTIPLY:
ListResults *= SingleCellOperations.PostProcessingValue;
break;
case eBinaryOperationType.DIVIDE:
ListResults /= SingleCellOperations.PostProcessingValue;
break;
default:
break;
}
}
#region Update the database
// create new column
SQLiteCommand mycommand = new SQLiteCommand(_SQLiteConnection);
String SQL = "ALTER TABLE \"" + item + "\" ADD COLUMN \"" + ColumnName + "\" REAL DEFAULT 0";
using (SQLiteCommand Command = new SQLiteCommand(SQL, _SQLiteConnection))
{
Command.ExecuteNonQuery();
}
// write data
using (SQLiteTransaction transaction = _SQLiteConnection.BeginTransaction())
using (SQLiteDataAdapter sqliteAdapter = new SQLiteDataAdapter("SELECT * FROM \"" + item + "\"", _SQLiteConnection))
{
DataSet DS = new DataSet();
sqliteAdapter.Fill(DS);
using (sqliteAdapter.InsertCommand = new SQLiteCommandBuilder(sqliteAdapter).GetUpdateCommand())
{
for (int i = 0; i < DS.Tables[0].Rows.Count; i++)
DS.Tables[0].Rows[i][ColumnName] = ListResults[i];
sqliteAdapter.Update(DS);
}
transaction.Commit();
}
#endregion
#region Update the screening data
cListSignature LDesc = new cListSignature();
cSignature NewSignature = new cSignature(ListResults, 256, NewDescType, cGlobalInfo.CurrentScreening);
LDesc.Add(NewSignature);
string[] Positions = item.Split('x');
cWell TmpWell = ListWell.GetFirstWell(int.Parse(Positions[1]), int.Parse(Positions[2]));
if(TmpWell!=null) TmpWell.AddSignatures(LDesc);
#endregion
NumTableProcessed++;
}
}
