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;
}
}
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;
}
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();
}
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 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;
}
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++;
}
}
/// <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++;
}
}
