// static cImageAccessor ImageAccessor;
public cSingleBiologicalObject(cCellularPhenotype CellularPhenotypeType, cWell AssociatedWell, int Idx)
{
// this.GlobalInfo = GlobalInfo;
// this.Class = Class;
this.CellularPhenotypeType = CellularPhenotypeType;
this.AssociatedWell = AssociatedWell;
}
// protected Size SizeHisto = new System.Drawing.Size(10, 5);
public cWell(cWell NewWell)
{
this.PosX = NewWell.PosX;
this.PosY = NewWell.PosY;
this.ListDescriptors = NewWell.ListDescriptors;
this.Parent = NewWell.Parent;
this.AssociatedChart = NewWell.AssociatedChart;
this.AssociatedPlate = NewWell.AssociatedPlate;
this.CurrentColor = this.Parent.GlobalInfo.GetColor(ClassForClassif);
}
public int AddWellToDataTable(cWell Well, DataTable DataTableToAddedTo, cGlobalInfo GlobalInfo)
{
SQLiteCommand mycommand = new SQLiteCommand(_SQLiteConnection);
mycommand.CommandText = "SELECT * FROM \"" + Well.SQLTableName + "\"";
SQLiteDataReader value = mycommand.ExecuteReader();
DataTable dt = new DataTable();
dt.Load(value);
List<string> Names = this.GetDescriptorNames(Well);
int CurrentClass = Well.GetCurrentClassIdx();
if (DataTableToAddedTo.Columns.Count == 0)
{
foreach (string TmpName in Names)
{
int DescIdx = cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorIndex(TmpName);
if ((DescIdx != -1) && (cGlobalInfo.CurrentScreening.ListDescriptors[DescIdx].IsActive()))
DataTableToAddedTo.Columns.Add(new DataColumn(TmpName, typeof(double)));
}
//if (IsAddWellClass)
// DataTableToAddedTo.Columns.Add(new DataColumn("Well_Class", typeof(int)));
}
for (int i = 0; i < dt.Rows.Count; i++)
{
DataTableToAddedTo.Rows.Add();
int RealIdxCol = 0;
for (int IdxCol = 0; IdxCol < Names.Count; IdxCol++)
{
int DescIdx = cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorIndex(Names[IdxCol]);
if ((DescIdx != -1) && (cGlobalInfo.CurrentScreening.ListDescriptors[DescIdx].IsActive()))
{
DataTableToAddedTo.Rows[DataTableToAddedTo.Rows.Count - 1][RealIdxCol++] = dt.Rows[i][IdxCol];
}
}
//if (IsAddWellClass)
// DataTableToAddedTo.Rows[DataTableToAddedTo.Rows.Count - 1][DataTableToAddedTo.Columns.Count - 1] = CurrentClass;
}
mycommand.Dispose();
mycommand = null;
value.Close();
value.Dispose();
value = null;
return dt.Rows.Count;
}
/// <summary>
/// Draw the dendogram signature for a specific well
/// </summary>
/// <param name="Well"></param>
/// <param name="Size"></param>
/// <param name="PosX"></param>
/// <param name="PosY"></param>
/// <returns>Lenght of the signature</returns>
private int DrawSignature(cWell Well, int Size, int PosX, int PosY)
{
int RealIdx = 0;
int SizeFont = Size / 4;
int ScrollShiftY = this.VerticalScroll.Value;
double Min, Max;
int ConvertedValue;
g.DrawString("[" + Well.GetPosX() + "x" + Well.GetPosY() + "]", new Font("Arial", 8), Brushes.Black, 15, PosY - ScrollShiftY);
Rectangle CurrentRect = new Rectangle(5, PosY, 8, Size);
SolidBrush CurrBrush = new SolidBrush(Well.GetClassColor());
// draw the rectangle
g.FillRectangle(CurrBrush, CurrentRect);
for (int iDesc = 0; iDesc < cGlobalInfo.CurrentScreening.ListDescriptors.Count; iDesc++)
{
if (!cGlobalInfo.CurrentScreening.ListDescriptors[iDesc].IsActive()) continue;
// specify the rect shape
CurrentRect = new Rectangle(PosX + RealIdx * Size, PosY, Size, Size);
// specify the color
cSignature CurrentDesc = Well.ListSignatures[iDesc];
byte[][] LUT = cGlobalInfo.CurrentPlateLUT;
Min = CurrentDendo.InfoForHierarchical.ListMin[RealIdx];
Max = CurrentDendo.InfoForHierarchical.ListMax[RealIdx];
if (Min == Max)
ConvertedValue = 0;
else
ConvertedValue = (int)(((CurrentDesc.GetValue() - Min) * (LUT[0].Length - 1)) / (Max - Min));
if (ConvertedValue >= LUT[0].Length) ConvertedValue = LUT[0].Length - 1;
CurrBrush = new SolidBrush(Color.FromArgb(LUT[0][ConvertedValue], LUT[1][ConvertedValue], LUT[2][ConvertedValue]));
// draw the rectangle
g.FillRectangle(CurrBrush, CurrentRect);
RealIdx++;
}
return PosX + RealIdx * Size;
}
public void ChangePhenotypeClass(cWell Well, cExtendedList ListNewClasses)
{
using (SQLiteTransaction transaction = _SQLiteConnection.BeginTransaction())
using (SQLiteDataAdapter sqliteAdapter = new SQLiteDataAdapter("SELECT * FROM \"" + Well.SQLTableName + "\"", _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]["Phenotype_Class"] = ListNewClasses[i];
sqliteAdapter.Update(DS);
}
transaction.Commit();
}
return;
}
public c3DWell(cPoint3D MinPt, cPoint3D MaxPt, Color Colour, cWell CurrentWell)
{
this.SetPosition(new cPoint3D(0, 0, 0));
this.Colour = Colour;
VTK_Cube = vtkCubeSource.New();
//VTK_Cube.SetBounds(MinPt.X, MaxPt.X, MinPt.Y, MaxPt.Y, MinPt.Z, MaxPt.Z);
VTK_Cube.SetXLength(MaxPt.X - MinPt.X);
VTK_Cube.SetYLength(MaxPt.Y - MinPt.Y);
VTK_Cube.SetZLength(MaxPt.Z - MinPt.Z);
vtk_PolyDataMapper = vtkPolyDataMapper.New();
vtk_PolyDataMapper.SetInputConnection(VTK_Cube.GetOutputPort());
this.SetPosition(MinPt);
this.Colour = Colour;
this.AssociatedWell = CurrentWell;
CreateVTK3DObject(1);
Information = new cInformation(this);
}
public FormForWellInformation(cWell CurrentWell)
{
InitializeComponent();
this.CurrentWell = CurrentWell;
}
//public cExtendedList GetWellPhenotypeClasses(string TableName)
//{
// cExtendedList ToReturn = new cExtendedList();
// SQLiteCommand mycommand = new SQLiteCommand(_SQLiteConnection);
// mycommand.CommandText = "SELECT *, \"" + "Phenotype_Class" + "\" FROM \"" + TableName + "\"";
// SQLiteDataReader value = mycommand.ExecuteReader();
// int Pos = value.GetOrdinal("Phenotype_Class");
// while (value.Read())
// ToReturn.Add(value.GetFloat(Pos));
// return ToReturn;
//}
public cListSingleBiologicalObjects GetBiologicalPhenotypes(cWell TmpWell)
{
cListSingleBiologicalObjects ToReturn = new cListSingleBiologicalObjects();
SQLiteCommand mycommand = new SQLiteCommand(_SQLiteConnection);
mycommand.CommandText = "SELECT *, \"" + "Phenotype_Class" + "\" FROM \"" + TmpWell.SQLTableName + "\"";
SQLiteDataReader value = mycommand.ExecuteReader();
int PosPhenotypeID = value.GetOrdinal("Phenotype_Class");
int PosPhenotypeConfidence = value.GetOrdinal("Phenotype_Confidence");
int PosPosX = value.GetOrdinal(cGlobalInfo.OptionsWindow.comboBoxDescriptorForPosX.Text);
int PosPosY = value.GetOrdinal(cGlobalInfo.OptionsWindow.comboBoxDescriptorForPosY.Text);
int BB_MinX = value.GetOrdinal(cGlobalInfo.OptionsWindow.comboBoxDescForBoundingMinX.Text);
int BB_MaxX = value.GetOrdinal(cGlobalInfo.OptionsWindow.comboBoxDescForBoundingMaxX.Text);
int BB_MinY = value.GetOrdinal(cGlobalInfo.OptionsWindow.comboBoxDescForBoundingMinY.Text);
int BB_MaxY = value.GetOrdinal(cGlobalInfo.OptionsWindow.comboBoxDescForBoundingMaxY.Text);
int PosField = value.GetOrdinal(cGlobalInfo.OptionsWindow.comboBoxDescriptorForField.Text);
int PosIdx = value.GetOrdinal("rowid");
if (PosPhenotypeID != -1)
{
while (value.Read())
{
string Res = value.GetValue(PosPhenotypeID).ToString();
if (Res == "") continue;
cSingleBiologicalObject NewPhenotype = new cSingleBiologicalObject(cGlobalInfo.ListCellularPhenotypes[(int)value.GetFloat(PosPhenotypeID)],
TmpWell, (int)value.GetFloat(PosIdx));
ToReturn.Add(NewPhenotype);
if (PosPhenotypeConfidence != -1)
NewPhenotype.ClassificationConfidence = (double)value.GetFloat(PosPhenotypeConfidence);
else
{
cGlobalInfo.WindowHCSAnalyzer.richTextBoxConsole.AppendText(TmpWell.AssociatedPlate.GetName() + " / " + TmpWell.GetPos() + ": Phenotype_Confidence column not found. Value set to null.");
NewPhenotype.ClassificationConfidence = 0;
}
if ((PosPosX != -1) && (PosPosY != -1))
ToReturn[ToReturn.Count - 1].Position = new _3D.cPoint3D(value.GetFloat(PosPosX), value.GetFloat(PosPosY), -1);
if ((BB_MinX != -1) && (BB_MinY != -1) && (BB_MaxX != -1) && (BB_MaxY != -1))
{
ToReturn[ToReturn.Count - 1].BD_BoxMin = new _3D.cPoint3D(value.GetFloat(BB_MinX), value.GetFloat(BB_MinY), -1);
ToReturn[ToReturn.Count - 1].BD_BoxMax = new _3D.cPoint3D(value.GetFloat(BB_MaxX), value.GetFloat(BB_MaxY), -1);
}
if (PosField != -1)
ToReturn[ToReturn.Count - 1].ImageField = (int)value.GetFloat(PosField);
}
}
else
{
while (value.Read())
{
cSingleBiologicalObject NewPhenotype = new cSingleBiologicalObject(cGlobalInfo.ListCellularPhenotypes[0], TmpWell, (int)value.GetFloat(PosIdx));
NewPhenotype.ClassificationConfidence = (double)value.GetFloat(PosPhenotypeConfidence);
ToReturn.Add(NewPhenotype);
if ((PosPosX != -1) && (PosPosY != -1))
ToReturn[ToReturn.Count - 1].Position = new _3D.cPoint3D(value.GetFloat(PosPosX), value.GetFloat(PosPosY), -1);
if (PosField != -1)
ToReturn[ToReturn.Count - 1].ImageField = (int)value.GetFloat(PosField);
}
}
mycommand.Dispose();
mycommand = null;
value.Close();
value.Dispose();
value = null;
return ToReturn;
}
public void LoadFromDisk(string Path)
{
if (ListWell == null)
{
cGlobalInfo.ConsoleWriteLine("ListWell NULL");
return;
}
IEnumerable<string> ListFile = Directory.EnumerateFiles(Path, "*.txt", SearchOption.TopDirectoryOnly);
int ProcessedWell = 0;
foreach (string FileName in ListFile)
{
cWell NewWell = new cWell(FileName, this.ParentScreening, this);
if (NewWell.GetPosX() != -1) ProcessedWell++;
this.AddWell(NewWell);
//ListWell[NewWell.GetPosX() - 1, NewWell.GetPosY() - 1] = NewWell;
}
ListMinMax = new List<double[]>();
for (int i = 0; i < ParentScreening.ListDescriptors.Count; i++)
{
double[] TmpMinMax = GetMinMax(i);
ListMinMax.Add(TmpMinMax);
}
this.NumberOfActiveWells = ProcessedWell;
cGlobalInfo.ConsoleWriteLine(ProcessedWell + " well(s) succesfully processed");
}
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();
}
void RenderWindow_RightButtonPressEvt(vtkObject sender, vtkObjectEventArgs e)
{
this.contextMenuStripActorPicker = new ContextMenuStrip();
int[] Pos;
Pos = this.iren.GetLastEventPosition();
ToolStripMenuItem ToolStripMenuItem_World = new ToolStripMenuItem("World");
ToolStripMenuItem ScaleItem = new ToolStripMenuItem("Scale");
ToolStripMenuItem_World.DropDownItems.Add(ScaleItem);
ScaleItem.Click += new System.EventHandler(this.ScaleClicking);
ToolStripMenuItem ColorItem = new ToolStripMenuItem("Background Color");
ToolStripMenuItem_World.DropDownItems.Add(ColorItem);
ColorItem.Click += new System.EventHandler(this.ColorClicking);
ToolStripMenuItem ExportViewItem = new ToolStripMenuItem("Export View");
ToolStripMenuItem_World.DropDownItems.Add(ExportViewItem);
ExportViewItem.Click += new System.EventHandler(this.ExportViewClicking);
if (this.ListNameObjectType.Count >= 1)
{
ToolStripMenuItem SelectionItem = new ToolStripMenuItem("Selection Type");
ToolStripMenuItem_World.DropDownItems.Add(SelectionItem);
SelectableObjectName = new List<bool>();
for (int idxName = 0; idxName < this.ListNameObjectType.Count; idxName++)
{
ToolStripMenuItem TypeName = new ToolStripMenuItem(ListNameObjectType[idxName]);
TypeName.CheckOnClick = true;
TypeName.Checked = true;
TypeName.Click += new System.EventHandler(this.TypeNameClicking);
if (TypeName.Checked) SelectableObjectName.Add(true);
else SelectableObjectName.Add(false);
}
}
string MetaObjectName = "";
vtkPicker Picker = vtkPicker.New();
int numActors = Picker.Pick(Pos[0], Pos[1], 0, this.ren1);
if (numActors == 1)
{
vtkActor PickedActor = Picker.GetActor();
bool selectable = false;
for (int i = 0; i < ListObject.Count; i++)
if (ListObject[i].GetActor() == PickedActor)
{
cInteractive3DObject Obj = (cInteractive3DObject)ListObject[i];
if (Obj.GetMetaObjectContainer() != null) MetaObjectName = Obj.GetMetaObjectContainer().Information.GetName() + " -> ";
for (int idx = 0; idx < this.SelectableObjectName.Count; idx++)
{
// the selected actor has been identified, let's get its type
cInteractive3DObject TmpBioObj = (cInteractive3DObject)ListObject[i];
int IdxType = -1;
for (int TmpIdx = 0; TmpIdx < this.ListNameObjectType.Count; TmpIdx++)
if (TmpBioObj.GetType() == this.ListNameObjectType[TmpIdx]) IdxType = TmpIdx;
// Is the type selectable (i.e. checked by the user in the contextual menu ?
if (this.SelectableObjectName[IdxType])
{
selectable = true;
break;
}
}
}
if (selectable == true)
{
ToolStripMenuItem TypeItem = null;
ToolStripMenuItem ToolStripMenuItem_ObjectDisplay = new ToolStripMenuItem("Object display");
// ToolStripMenuItem CentroidItem = new ToolStripMenuItem("Centroid");
ToolStripMenuItem ToolStripMenuItem_MetaDescriptorDisplay = null;
ToolStripMenuItem_DescriptorDisplay = new ToolStripMenuItem("Object profil");
{
for (int i = 0; i < ListObject.Count; i++)
if (ListObject[i].GetActor() == PickedActor)
{
Type T = ListObject[i].GetType();
List<double> ListDesc = null;
List<string> ListProfilName = null;
if (T.Name == "cBiological3DVolume")
{
cBiological3DVolume TmpVol = (cBiological3DVolume)ListObject[i];
ListProfilName = TmpVol.Information.GetDescriptorNames();
ListDesc = TmpVol.Information.GetInformation();
TypeItem = new ToolStripMenuItem(MetaObjectName + TmpVol.GetType());
}
else if (T.Name == "cBiologicalSpot")
{
cBiologicalSpot TmpSpot = (cBiologicalSpot)ListObject[i];
ListProfilName = TmpSpot.Information.GetDescriptorNames();
ListDesc = TmpSpot.Information.GetInformation();
TypeItem = new ToolStripMenuItem(MetaObjectName + TmpSpot.GetType());
}
else if (T.Name == "c3DWell")
{
c3DWell TmpWell = (c3DWell)ListObject[i];
ListProfilName = TmpWell.Information.GetDescriptorNames();
ListDesc = TmpWell.Information.GetInformation();
TypeItem = new ToolStripMenuItem(MetaObjectName + TmpWell.GetType());
Chart ThumbnailChart = TmpWell.AssociatedWell.GetChart();
if (ThumbnailChart != null)
{
MemoryStream ms = new MemoryStream();
TmpWell.AssociatedWell.GetChart().SaveImage(ms, ChartImageFormat.Bmp);
TypeItem.Image = new Bitmap(ms);
TypeItem.ImageScaling = ToolStripItemImageScaling.None;
TypeItem.Size = new System.Drawing.Size(48, 48);
// New3DWell.ThumbnailnewImage = new Bitmap(ms);
}
CurrentlySelectedWell = TmpWell.AssociatedWell;
TypeItem.Click += new System.EventHandler(this.WellInfoClick);
}
else if (T.Name == "c3DIsoContours")
{
c3DIsoContours TmpContours = (c3DIsoContours)ListObject[i];
// ListProfilName = TmpWell.Information.GetDescriptorNames();
// ListDesc = TmpWell.Information.GetInformation();
TypeItem = new ToolStripMenuItem();
Chart TmpChart = new Chart();
Series SeriesPos = new Series();
//SeriesPos.ShadowOffset = 1;
ChartArea CurrentChartArea = new ChartArea();
List<double> DoubleList = new List<double>();
int Idx = 0;
double[] Colour =TmpContours.GetActor().GetProperty().GetColor();
foreach (cPoint3D CurrentPt in TmpContours.ListPtContour)
{
SeriesPos.Points.AddY(CurrentPt.Z);
SeriesPos.Points[Idx].MarkerSize = 2;
SeriesPos.Points[Idx].MarkerStyle = MarkerStyle.Circle;
SeriesPos.Points[Idx++].Color = Color.FromArgb((int)Colour[0], (int)Colour[1], (int)Colour[2]);
//DoubleList.Add(CurrentPt.Z);
}
//CDisplayGraph DispGraph = new CDisplayGraph(DoubleList.ToArray());
SeriesPos.ChartType = SeriesChartType.Point;
TmpChart.ChartAreas.Add(CurrentChartArea);
CurrentChartArea.Axes[1].LabelStyle.Enabled = false;
CurrentChartArea.Axes[1].MajorGrid.Enabled = false;
CurrentChartArea.Axes[0].Enabled = AxisEnabled.False;
CurrentChartArea.Axes[1].Enabled = AxisEnabled.False;
CurrentChartArea.Axes[0].MajorGrid.Enabled = false;
TmpChart.Width = 120;
TmpChart.Height = 60;
TmpChart.TextAntiAliasingQuality = TextAntiAliasingQuality.High;
TmpChart.Series.Add(SeriesPos);
//Chart ThumbnailChart = TmpChart.NewWindow.chartForSimpleForm;
// if (ThumbnailChart != null)
{
MemoryStream ms = new MemoryStream();
TmpChart.SaveImage(ms, ChartImageFormat.Bmp);
TypeItem.Image = new Bitmap(ms);
TypeItem.ImageScaling = ToolStripItemImageScaling.None;
TypeItem.Size = new System.Drawing.Size(48, 48);
// New3DWell.ThumbnailnewImage = new Bitmap(ms);
}
// CurrentlySelectedWell = TmpWell.AssociatedWell;
// TypeItem.Click += new System.EventHandler(this.WellInfoClick);
}
if (((cInteractive3DObject)ListObject[i]).ThumbnailnewImage != null)
{
// TypeItem.Image = ((cBiological3DObject)ListObject[i]).ThumbnailnewImage;
// TypeItem.ImageScaling = ToolStripItemImageScaling.None;
// TypeItem.Size = new System.Drawing.Size(48, 48);
// TypeItem.Click += new System.EventHandler(this.WellInfoClick);
}
if (ListProfilName != null)
for (int idxName = 0; idxName < ListProfilName.Count; idxName++)
{
ToolStripMenuItem descName = new ToolStripMenuItem(ListProfilName[idxName] + " : " + ListDesc[idxName]);
ToolStripMenuItem_DescriptorDisplay.DropDownItems.Add(descName);
}
else
{
ToolStripMenuItem descName = new ToolStripMenuItem("Null");
ToolStripMenuItem_DescriptorDisplay.DropDownItems.Add(descName);
}
}
}
ToolStripSeparator SepratorStrip = new ToolStripSeparator();
if (ToolStripMenuItem_MetaDescriptorDisplay != null)
contextMenuStripActorPicker.Items.AddRange(new ToolStripItem[] { TypeItem, SepratorStrip, ToolStripMenuItem_World, ToolStripMenuItem_ObjectDisplay, ToolStripMenuItem_DescriptorDisplay, ToolStripMenuItem_MetaDescriptorDisplay });
else
contextMenuStripActorPicker.Items.AddRange(new ToolStripItem[] { TypeItem, SepratorStrip, ToolStripMenuItem_World, ToolStripMenuItem_ObjectDisplay, ToolStripMenuItem_DescriptorDisplay });
}
else
contextMenuStripActorPicker.Items.AddRange(new ToolStripItem[] { ToolStripMenuItem_World });
}
else
contextMenuStripActorPicker.Items.AddRange(new ToolStripItem[] { ToolStripMenuItem_World });
int[] PosWindow = this.renWin.GetSize();
contextMenuStripActorPicker.Show(Control.MousePosition);
return;
}
public List<string> GetDescriptorNames(cWell Well)
{
List<string> ToReturn = new List<string>();
// string NameWell = GetListTableNames()[IdxWell];
SQLiteCommand mycommand = new SQLiteCommand(_SQLiteConnection);
mycommand.CommandText = "SELECT * FROM \"" + Well.SQLTableName + "\"";
SQLiteDataReader value = mycommand.ExecuteReader();
for (int i = 0; i < value.FieldCount; i++)
ToReturn.Add(value.GetName(i));
return ToReturn;
}
private void generateDRCsToolStripMenuItem_Click(object sender, EventArgs e)
{
int nbrofdrugs = 6;
int nbrofconcentrations = 10;
int nbrofdesc = 3;
double[, ,] DRC = new double[nbrofconcentrations, nbrofdrugs, nbrofdesc];
float[] X1 = new float[nbrofconcentrations];
X1[0] = 1000;
for (int i = 1; i < X1.Length; i++)
{
X1[i] = X1[i - 1] / 3;
}
Random Bot = new Random();
Random To = new Random();
Random Ec5 = new Random();
Random Slop = new Random();
CompleteScreening = new cScreening("Current Screen", this.GlobalInfo);
CompleteScreening.Columns = nbrofconcentrations;
CompleteScreening.Rows = nbrofdrugs;
for (int j = 0; j < nbrofdrugs; j++)
{
for (int k = 0; k < nbrofdesc; k++)
{
float Bottom = Bot.Next(10);
float Top = To.Next(80, 100);
float Ec50 = Ec5.Next(40, 60);
float Slope = Slop.Next(1, 5);
for (int i = 0; i < X1.Length; i++)
{
//DRC[i, j, k] = Bottom + (Top - Bottom) / (1 + Math.Pow(((Math.Pow(10, Ec50) / Math.Pow(10, X1[0]))), Slope));
DRC[i, j, k] = Bottom + (Top - Bottom) / (1 + Math.Pow((X1[i] / Ec50), -Slope));
}
}
}
cPlate NewPlate = new cPlate("Cpds", "Plate0", CompleteScreening);
CompleteScreening.AddPlate(NewPlate);
CompleteScreening.ListDescriptors.Clean();
for (int k = 0; k < nbrofdesc; k++)
{
cDescriptorsType DescType = new cDescriptorsType("Desc" + k, true, 1, GlobalInfo);
CompleteScreening.ListDescriptors.AddNew(DescType);
}
for (int j = 0; j < nbrofdrugs; j++)
{
for (int i = 0; i < nbrofconcentrations; i++)
{
List<cDescriptor> LDesc = new List<cDescriptor>();
for (int k = 0; k < nbrofdesc; k++)
{
//DRC[i, j, k] = Bottom + (Top - Bottom) / (1 + Math.Pow(((Math.Pow(10, Ec50) / Math.Pow(10, X1[0]))), Slope));
cDescriptor CurrentDesc = new cDescriptor(DRC[i, j, k], CompleteScreening.ListDescriptors[k], CompleteScreening);
LDesc.Add(CurrentDesc);
}
cWell NewWell = new cWell(LDesc, i+1, j+1, CompleteScreening, NewPlate);
NewWell.Concentration = X1[i];
NewPlate.AddWell(NewWell);
}
}
CompleteScreening.ListDescriptors.UpDateDisplay();
CompleteScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < CompleteScreening.ListPlatesActive.Count; idxP++)
CompleteScreening.ListPlatesActive[idxP].UpDataMinMax();
StartingUpDateUI();
this.toolStripcomboBoxPlateList.Items.Clear();
for (int IdxPlate = 0; IdxPlate < CompleteScreening.ListPlatesActive.Count; IdxPlate++)
{
string Name = CompleteScreening.ListPlatesActive.GetPlate(IdxPlate).Name;
this.toolStripcomboBoxPlateList.Items.Add(Name);
PlateListWindow.listBoxPlateNameToProcess.Items.Add(Name);
PlateListWindow.listBoxAvaliableListPlates.Items.Add(Name);
}
CompleteScreening.CurrentDisplayPlateIdx = 0;
CompleteScreening.SetSelectionType(comboBoxClass.SelectedIndex - 1);
UpdateUIAfterLoading();
}
public cExtendedTable GetWellValues(cWell TmpWell, List<cDescriptorType> ListDescType, List<cCellularPhenotype> PhenotypesToBeSelected, double PopulationRatio)
{
cExtendedTable ToReturn = new cExtendedTable();
foreach (var item in ListDescType)
{
cExtendedList TmpList = new cExtendedList();
TmpList.Name = item.GetName();
TmpList.Tag = item;
TmpList.ListTags = new List<object>();
SQLiteCommand mycommand = new SQLiteCommand(_SQLiteConnection);
mycommand.CommandText = "SELECT \"" + item.GetName() + "\" FROM \"" + TmpWell.SQLTableName + "\" WHERE Phenotype_Class IN (";
foreach (var PhenotypeClass in PhenotypesToBeSelected)
{
mycommand.CommandText += PhenotypeClass.Idx + ",";
}
mycommand.CommandText = mycommand.CommandText.Remove(mycommand.CommandText.Length - 1);
mycommand.CommandText += ")";
//mycommand.CommandText = "SELECT *, FROM \"" + TableName + "\"";
SQLiteDataReader value = mycommand.ExecuteReader();
// value.Read();
int Pos = value.GetOrdinal(item.GetName());
if (Pos == -1) continue;
while (value.Read())
{
TmpList.Add(value.GetFloat(Pos));
}
cExtendedList SubListToBeTransfered = new cExtendedList(TmpList, PopulationRatio);
ToReturn.Add(SubListToBeTransfered);
mycommand.Dispose();
mycommand = null;
value.Close();
value.Dispose();
value = null;
}
return ToReturn;
}
public cExtendedTable GetWellValues(cWell TmpWell, List<cDescriptorType> ListDescType)
{
cExtendedTable ToReturn = new cExtendedTable();
ToReturn.ListTags = new List<object>();
foreach (var item in ListDescType)
{
cExtendedList TmpList = new cExtendedList();
TmpList.Name = item.GetName();
TmpList.Tag = item;
TmpList.ListTags = new List<object>();
SQLiteCommand mycommand = new SQLiteCommand(_SQLiteConnection);
mycommand.CommandText = "SELECT \"" + item.GetName() + "\" FROM \"" + TmpWell.SQLTableName + "\" ";
//mycommand.CommandText = "SELECT *, FROM \"" + TableName + "\"";
SQLiteDataReader value = mycommand.ExecuteReader();
// value.Read();
int Pos = value.GetOrdinal(item.GetName());
if (Pos == -1) continue;
if (value.GetValue(Pos).ToString() == "") continue;
while (value.Read())
{
TmpList.Add(value.GetFloat(Pos));
}
ToReturn.Add(TmpList);
mycommand.Dispose();
mycommand = null;
value.Close();
value.Dispose();
value = null;
}
return ToReturn;
}
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 cExtendedTable GetWellPhenotypeId(cWell TmpWell, List<cCellularPhenotype> PhenotypesToBeSelected)
{
cExtendedTable ToReturn = new cExtendedTable();
// foreach (var item in ListDescType)
// {
cExtendedList TmpList = new cExtendedList();
TmpList.Name = "Phenotype_Class";
//TmpList.Tag = item;
TmpList.ListTags = new List<object>();
SQLiteCommand mycommand = new SQLiteCommand(_SQLiteConnection);
if (PhenotypesToBeSelected != null)
{
mycommand.CommandText = "SELECT \"" + "Phenotype_Class" + "\" FROM \"" + TmpWell.SQLTableName + "\" WHERE Phenotype_Class IN (";
foreach (var PhenotypeClass in PhenotypesToBeSelected)
{
mycommand.CommandText += PhenotypeClass.Idx + ",";
}
mycommand.CommandText = mycommand.CommandText.Remove(mycommand.CommandText.Length - 1);
mycommand.CommandText += ")";
}
else
{
mycommand.CommandText = "SELECT \"" + "Phenotype_Class" + "\" FROM \"" + TmpWell.SQLTableName + "\"";
}
//mycommand.CommandText = "SELECT *, FROM \"" + TableName + "\"";
SQLiteDataReader value = mycommand.ExecuteReader();
// value.Read();
int Pos = value.GetOrdinal("Phenotype_Class");
if (Pos != -1)
{
while (value.Read()) TmpList.Add(value.GetFloat(Pos));
}
ToReturn.Add(TmpList);
mycommand.Dispose();
mycommand = null;
value.Close();
value.Dispose();
value = null;
// }
return ToReturn;
//cExtendedTable ToReturn = new cExtendedTable();
//cExtendedList TmpList = new cExtendedList();
//SQLiteCommand mycommand = new SQLiteCommand(_SQLiteConnection);
//mycommand.CommandText = "SELECT *, \"" + "Phenotype_Class" + "\" FROM \"" + TmpWell.SQLTableName + "\"";
//SQLiteDataReader value = mycommand.ExecuteReader();
//int PosPhenotypeID = value.GetOrdinal("Phenotype_Class");
//cExtendedList ListErrorsIdx = new cExtendedList("List Error Indexes - " + TmpWell.Name);
//int IdxRow = 0;
////if (Pos == -1) continue;
//while (value.Read())
//{
// if (value.GetValue(PosPhenotypeID).ToString() != "")
// {
// TmpList.Add(value.GetDouble(PosPhenotypeID));
// }
// else
// {
// TmpList.Add(0);
// ListErrorsIdx.Add(IdxRow);
// }
// IdxRow++;
//}
//ToReturn.Add(TmpList);
//return ToReturn;
}
public int GetNumberOfRows(cWell Well)
{
SQLiteCommand mycommand = new SQLiteCommand(_SQLiteConnection);
mycommand.CommandText = "SELECT COUNT(*) FROM " + Well.SQLTableName;
try
{
SQLiteDataReader value = mycommand.ExecuteReader();
int ToReturn = 0;
while (value.Read())
{
ToReturn = value.GetInt32(0);
}
mycommand.Dispose();
mycommand = null;
value.Close();
value.Dispose();
value = null;
return ToReturn;
}
catch
{
mycommand.Dispose();
mycommand = null;
return -1;
}
}
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 (CompleteScreening != null) CompleteScreening.Close3DView();
// CompleteScreening.ListDescriptors.RemoveDesc(CompleteScreening.ListDescriptors[IntToTransfer], CompleteScreening);
cScreening MergedScreening = new cScreening("Merged Screen", GlobalInfo);
MergedScreening.PanelForPlate = this.panelForPlate;
MergedScreening.Rows = CompleteScreening.Rows;
MergedScreening.Columns = CompleteScreening.Columns;
MergedScreening.ListPlatesAvailable = new cExtendPlateList();
// create the descriptor
MergedScreening.ListDescriptors.Clean();
int Idesc = 0;
List<cDescriptorsType> ListDescType = new List<cDescriptorsType>();
for (int i = 0; i < CompleteScreening.ListDescriptors.Count; i++)
{
if (!CompleteScreening.ListDescriptors[i].IsActive()) continue;
cDescriptorsType DescEC50 = new cDescriptorsType("EC50_" + CompleteScreening.ListDescriptors[i].GetName(), true, 1, GlobalInfo);
ListDescType.Add(DescEC50);
MergedScreening.ListDescriptors.AddNew(DescEC50);
cDescriptorsType DescTop = new cDescriptorsType("Top_" + CompleteScreening.ListDescriptors[i].GetName(), true, 1, GlobalInfo);
ListDescType.Add(DescTop);
MergedScreening.ListDescriptors.AddNew(DescTop);
cDescriptorsType DescBottom = new cDescriptorsType("Bottom_" + CompleteScreening.ListDescriptors[i].GetName(), true, 1, GlobalInfo);
ListDescType.Add(DescBottom);
MergedScreening.ListDescriptors.AddNew(DescBottom);
cDescriptorsType DescSlope = new cDescriptorsType("Slope_" + CompleteScreening.ListDescriptors[i].GetName(), true, 1, GlobalInfo);
ListDescType.Add(DescSlope);
MergedScreening.ListDescriptors.AddNew(DescSlope);
Idesc++;
}
MergedScreening.ListDescriptors.CurrentSelectedDescriptor = 0;
foreach (cPlate CurrentPlate in CompleteScreening.ListPlatesAvailable)
{
cPlate NewPlate = new cPlate("Cpds", CurrentPlate.Name + " Merged", MergedScreening);
// check if the plate exist already
MergedScreening.AddPlate(NewPlate);
foreach (cDRC_Region CurrentRegion in CurrentPlate.ListDRCRegions)
{
List<cDescriptor> LDesc = new List<cDescriptor>();
Idesc = 0;
int IDESCBase = 0;
for (int i = 0; i < CompleteScreening.ListDescriptors.Count; i++)
{
if (!CompleteScreening.ListDescriptors[i].IsActive()) continue;
cDRC CurrentDRC = CurrentRegion.GetDRC(CompleteScreening.ListDescriptors[IDESCBase++]);
cDescriptor Desc_EC50 = new cDescriptor(CurrentDRC.EC50, ListDescType[Idesc++], CompleteScreening);
LDesc.Add(Desc_EC50);
cDescriptor Desc_Top = new cDescriptor(CurrentDRC.Top, ListDescType[Idesc++], CompleteScreening);
LDesc.Add(Desc_Top);
cDescriptor Desc_Bottom = new cDescriptor(CurrentDRC.Bottom, ListDescType[Idesc++], CompleteScreening);
LDesc.Add(Desc_Bottom);
cDescriptor Desc_Slope = new cDescriptor(CurrentDRC.Slope, ListDescType[Idesc++], CompleteScreening);
LDesc.Add(Desc_Slope);
}
cWell NewWell = new cWell(LDesc, CurrentRegion.PosXMin + 1, CurrentRegion.PosYMin + 1, MergedScreening, NewPlate);
NewWell.Name = "DRC [" + CurrentRegion.PosXMin + ":" + CurrentRegion.PosYMin + "]";
NewPlate.AddWell(NewWell);
}
}
// PanelList[0].CurrentScreening.ListPlatesActive.Clear();
// PanelList[0].CurrentScreening.GlobalInfo.WindowHCSAnalyzer.RefreshInfoScreeningRichBox();
MergedScreening.ListPlatesActive = new cExtendPlateList();
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);
CompleteScreening.ListDescriptors = MergedScreening.ListDescriptors;
CompleteScreening.ListPlatesAvailable = MergedScreening.ListPlatesAvailable;
CompleteScreening.ListPlatesActive = MergedScreening.ListPlatesActive;
CompleteScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < CompleteScreening.ListPlatesActive.Count; idxP++)
CompleteScreening.ListPlatesActive[idxP].UpDataMinMax();
CompleteScreening.GetCurrentDisplayPlate().DisplayDistribution(CompleteScreening.ListDescriptors.CurrentSelectedDescriptor, true);
}
public double DistanceTo(cWell DestinationWell, int Idxdescriptor, eDistances DistanceType)
{
double Distance = 0;
switch (DistanceType)
{
case eDistances.EUCLIDEAN:
Distance = this.ListSignatures[Idxdescriptor].GetHistovalues().Dist_Euclidean(DestinationWell.ListSignatures[Idxdescriptor].GetHistovalues());
break;
case eDistances.MANHATTAN:
Distance = this.ListSignatures[Idxdescriptor].GetHistovalues().Dist_Manhattan(DestinationWell.ListSignatures[Idxdescriptor].GetHistovalues());
break;
case eDistances.VECTOR_COS:
Distance = this.ListSignatures[Idxdescriptor].GetHistovalues().Dist_VectorCosine(DestinationWell.ListSignatures[Idxdescriptor].GetHistovalues());
break;
case eDistances.BHATTACHARYYA:
Distance = this.ListSignatures[Idxdescriptor].GetHistovalues().Dist_BhattacharyyaCoefficient(DestinationWell.ListSignatures[Idxdescriptor].GetHistovalues());
break;
case eDistances.EMD:
Distance = this.ListSignatures[Idxdescriptor].GetHistovalues().Dist_EarthMover(DestinationWell.ListSignatures[Idxdescriptor].GetHistovalues());
break;
default:
break;
}
return Distance;
}
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 double DistanceTo(cWell DestinationWell, eDistances DistanceType)
{
double Distance = 0;
switch (DistanceType)
{
case eDistances.EUCLIDEAN:
Distance += this.GetAverageValuesList(true)[0].Dist_Euclidean(DestinationWell.GetAverageValuesList(true)[0]);
break;
case eDistances.MANHATTAN:
Distance += this.GetAverageValuesList(true)[0].Dist_Manhattan(DestinationWell.GetAverageValuesList(true)[0]);
break;
case eDistances.VECTOR_COS:
Distance += this.GetAverageValuesList(true)[0].Dist_VectorCosine(DestinationWell.GetAverageValuesList(true)[0]);
break;
case eDistances.BHATTACHARYYA:
Distance += this.GetAverageValuesList(true)[0].Dist_BhattacharyyaCoefficient(DestinationWell.GetAverageValuesList(true)[0]);
break;
case eDistances.EMD:
Distance += this.GetAverageValuesList(true)[0].Dist_EarthMover(DestinationWell.GetAverageValuesList(true)[0]);
break;
default:
break;
}
return Distance;
}
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);
}
public double DistanceTo(cWell DestinationWell, eDistances IntraHistoDistanceType, eDistances InterHistoDistanceType)
{
double Distance = 0;
cExtendedList ListDistSource = new cExtendedList();
cExtendedList ListDistDest = new cExtendedList();
for (int Idxdescriptor = 0; Idxdescriptor < cGlobalInfo.CurrentScreening.ListDescriptors.Count; Idxdescriptor++)
{
if (cGlobalInfo.CurrentScreening.ListDescriptors[Idxdescriptor].IsActive() == false) continue;
switch (IntraHistoDistanceType)
{
case eDistances.EUCLIDEAN:
ListDistSource.Add(this.ListSignatures[Idxdescriptor].GetHistovalues().Dist_Euclidean(DestinationWell.ListSignatures[Idxdescriptor].GetHistovalues()));
ListDistDest.Add(DestinationWell.ListSignatures[Idxdescriptor].GetValue());
Distance = ListDistSource.Dist_Euclidean(ListDistDest);
break;
case eDistances.MANHATTAN:
Distance = ListDistSource.Dist_Manhattan(ListDistDest);
break;
case eDistances.VECTOR_COS:
Distance = ListDistSource.Dist_VectorCosine(ListDistDest);
break;
case eDistances.BHATTACHARYYA:
Distance = ListDistSource.Dist_BhattacharyyaCoefficient(ListDistDest);
break;
case eDistances.EMD:
Distance = ListDistSource.Dist_EarthMover(ListDistDest);
break;
default:
break;
}
}
switch (InterHistoDistanceType)
{
case eDistances.EUCLIDEAN:
Distance = ListDistSource.Dist_Euclidean(ListDistDest);
break;
case eDistances.MANHATTAN:
Distance = ListDistSource.Dist_Manhattan(ListDistDest);
break;
case eDistances.VECTOR_COS:
Distance = ListDistSource.Dist_VectorCosine(ListDistDest);
break;
case eDistances.BHATTACHARYYA:
Distance = ListDistSource.Dist_BhattacharyyaCoefficient(ListDistDest);
break;
case eDistances.EMD:
Distance = ListDistSource.Dist_EarthMover(ListDistDest);
break;
default:
break;
}
return Distance;
}
public bool AddWell(cWell NewWell)
{
int PosX = NewWell.GetPosX() - 1;
int PosY = NewWell.GetPosY() - 1;
try
{
ListWell[PosX, PosY] = NewWell;
ListActiveWells.Add(NewWell);
ListWells.Add(NewWell);
}
catch (Exception)
{
return false;
}
return true;
}
public void DisplayTable(cWell Well)
{
SQLiteCommand mycommand = new SQLiteCommand(_SQLiteConnection);
mycommand.CommandText = "SELECT * FROM \"" + Well.SQLTableName + "\"";
SQLiteDataReader value = mycommand.ExecuteReader();
DataTable dt = new DataTable();
dt.Load(value);
cDisplayScatter2D WindowForTable = new cDisplayScatter2D(dt);
WindowForTable.comboBoxAxeX.DataSource = this.GetDescriptorNames(Well);
WindowForTable.comboBoxAxeY.DataSource = this.GetDescriptorNames(Well);
WindowForTable.comboBoxVolume.DataSource = this.GetDescriptorNames(Well);
WindowForTable.chartForPoints.Series[0].MarkerColor = Well.GetClassColor();
// WindowForTable.ch
WindowForTable.Text = Well.AssociatedPlate.GetName() + " [" + Well.GetPosX() + "x" + Well.GetPosY() + "]";
WindowForTable.Show();
}
