public cFeedBackMessage Run(c3DNewWorld _3DWorld)
{
if (this.Input == null)
{
FeedBackMessage.IsSucceed = false;
FeedBackMessage.Message = "No input data table defined.";
return FeedBackMessage;
}
ListObjects = new cListGeometric3DObject("Plate MetaObject");
cImage I = this.Input.GetClassColorImage();
// cDisplaySingleImage DSI = new cDisplaySingleImage();
// DSI.SetInputData(I);
// DSI.Run();
c3DTexturedPlan PlateTexture = new c3DTexturedPlan(new cPoint3D(0, 0, 0), I);
//c3DTexturedPlan PlateTexture = new c3DTexturedPlan(new cPoint3D(0,0,0),this.Input.GetColorImage());
PlateTexture.SetName(Input.GetShortInfo());
PlateTexture.Tag = this.Input;
// List<byte[][]> TmpLut = new List<byte[][]>();
// TmpLut.Add(cGlobalInfo.CurrentPlateLUT);
// PlateTexture.LUT = TmpLut ;
PlateTexture.Run();
ListObjects.AddObject(PlateTexture);
ListObjects[0].Tag = ListObjects.Tag = this.Input;
ListObjects.AddObject(new c3DText(this.Input.GetName(), new cPoint3D(-12-1.2, -8-1.2, 0.2), Color.Black, 70));
return base.FeedBackMessage;
}
public Form3DTreeView(c3DNewWorld AssociatedWorld)
{
InitializeComponent();
this.AssociatedWorld = AssociatedWorld;
this.treeViewFor3DObjects.NodeMouseClick += new TreeNodeMouseClickEventHandler(treeViewFor3DObjects_NodeMouseClick);
this.treeViewFor3DObjects.MouseDown += new MouseEventHandler(treeViewFor3DObjects_MouseDown);
RefreshTree();
}
public cFeedBackMessage Run(c3DNewWorld _3DWorld)
{
if (this.Input == null)
{
FeedBackMessage.IsSucceed = false;
FeedBackMessage.Message = "No input data table defined.";
return FeedBackMessage;
}
ListObjects = new cListGeometric3DObject("Screening MetaObject");
int IdxPlate = 0;
int Pos = 0;
foreach (cPlate item in this.Input.ListPlatesActive)
{
c3DObject_Plate2D P2D = new c3DObject_Plate2D();
P2D.SetInputData(item);
P2D.Run(_3DWorld);
foreach (var itemObj in P2D.GetOutPut())
{
cPoint3D CurrentObjPos = itemObj.GetPosition() + new cPoint3D(Pos, 0, 0);
itemObj.SetPosition(CurrentObjPos);
}
//P2D.GetOutPut()[0].Tag = item;
Pos += this.Input.Columns + 10;
//c3DTexturedPlan PlateTexture = new c3DTexturedPlan(new cPoint3D(0,0,0),this.Input.GetColorImage());
//PlateTexture.SetName(Input.());
//PlateTexture.Tag = this.Input;
//List<byte[][]> TmpLut = new List<byte[][]>();
//TmpLut.Add(cGlobalInfo.CurrentPlateLUT);
//PlateTexture.LUT = TmpLut ;
//PlateTexture.Run();
foreach (var itemObj in P2D.GetOutPut())
{
ListObjects.AddObject(itemObj);
}
IdxPlate++;
}
ListObjects.Tag = this.Input;
return base.FeedBackMessage;
}
public cFeedBackMessage Run(c3DNewWorld _3DWorld)
{
if (base.Start() == false)
{
base.FeedBackMessage.IsSucceed = false;
return base.FeedBackMessage;
}
//if (this.Input == null)
//{
// FeedBackMessage.IsSucceed = false;
// FeedBackMessage.Message = "No input data table defined.";
// return FeedBackMessage;
//}
#region Properties Management
object _firstValue = base.ListProperties.FindByName("Normalized ?");
bool IsNormalized = false;
if (_firstValue == null)
{
base.GenerateError("-Normalized ?- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
IsNormalized = (bool)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Normalized ?- cast didn't work");
return base.FeedBackMessage;
}
_firstValue = base.ListProperties.FindByName("Draw Axis ?");
bool IsdrawAxis = true;
if (_firstValue == null)
{
base.GenerateError("-Draw Axis ?- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
IsdrawAxis = (bool)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Draw Axis ?- cast didn't work");
return base.FeedBackMessage;
}
_firstValue = base.ListProperties.FindByName("Link Points ?");
bool IsLinked = false;
if (_firstValue == null)
{
base.GenerateError("-Link Points ?- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
IsLinked = (bool)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Link Points ?- cast didn't work");
return base.FeedBackMessage;
}
#endregion
cExtendedList ListLenghtsMax = new cExtendedList();
ListObjects = new cListGeometric3DObject("Scatter Plot MetaObject");
double MinX = this.Input.Min(0);
double MaxX = this.Input.Max(0);
double DeltaX = MaxX - MinX;
ListLenghtsMax.Add(DeltaX);
if (DeltaX == 0) DeltaX = 1;
double MinY = this.Input.Min(1);
double MaxY = this.Input.Max(1);
double DeltaY = MaxY - MinY;
ListLenghtsMax.Add(DeltaY);
if (DeltaY == 0) DeltaY = 1;
double MinZ = this.Input.Min(2);
double MaxZ = this.Input.Max(2);
double DeltaZ = MaxZ - MinZ;
ListLenghtsMax.Add(DeltaZ);
if (DeltaZ == 0) DeltaZ = 1;
double MinRad = 0;
double MaxRad = 0;
double DeltaRad = 1;
double MaxLenght = ListLenghtsMax.Min();
if (MaxLenght <= 0) MaxLenght = 1;
for (int CurrentSerie = 0; CurrentSerie < this.Input.Count; CurrentSerie++)
{
cExtendedTable CurrentTable = this.Input[CurrentSerie];
if ((IndexColumnForSphereRadius > 0) && (IndexColumnForSphereRadius < CurrentTable.Count))
{
MinRad = CurrentTable[IndexColumnForSphereRadius].Min();
MaxRad = CurrentTable[IndexColumnForSphereRadius].Max();
if (MaxRad != MinRad)
DeltaRad = MaxRad - MinRad;
}
if (CurrentTable.Count == 0) continue;
cListGeometric3DObject TmpListObjects = new cListGeometric3DObject("Scatter MetaObject");
TmpListObjects.Tag = CurrentTable.Tag;
cPoint3D Pt = null;
for (int IdxPt = 0; IdxPt < CurrentTable[0].Count; IdxPt++)
{
if(IsNormalized)
Pt = new cPoint3D((CurrentTable[0][IdxPt] - MinX) / DeltaX, (CurrentTable[1][IdxPt] - MinY) / DeltaY, (CurrentTable[2][IdxPt] - MinZ) / DeltaZ);
else
Pt = new cPoint3D(CurrentTable[0][IdxPt], CurrentTable[1][IdxPt], CurrentTable[2][IdxPt]);
double Rad = this.Radius;
if ((IndexColumnForSphereRadius > 0) && (IndexColumnForSphereRadius < CurrentTable.Count))
{
Rad = this.Radius * ((CurrentTable[IndexColumnForSphereRadius][IdxPt] - MinRad)) / DeltaRad;
Rad /= 200;
}
if(IndexColumnForSphereRadius>-1)
Rad = CurrentTable[IndexColumnForSphereRadius][IdxPt];
if (IsNormalized) Rad /= 300.0;
else
{
Rad = MaxLenght / 100.0;
}
c3DSphere Sphere = new c3DSphere(Pt, Rad);
//c3DPoint Sphere = new c3DPoint(Pt);
if ((CurrentTable.ListRowNames != null) && (CurrentTable.ListRowNames.Count > IdxPt))
{
if (CurrentTable.ListRowNames[IdxPt] != null) Sphere.SetName(CurrentTable.ListRowNames[IdxPt]);
else
Sphere.SetName("Sphere " + IdxPt);
}
else
{
Sphere.SetName("Sphere " + IdxPt);
}
if ((CurrentTable.ListTags != null) && (CurrentTable.ListTags[IdxPt] != null) && (CurrentTable.ListTags[IdxPt].GetType() == typeof(cWell)))
{
if (CurrentTable.ListTags[IdxPt].GetType() == typeof(cWell))
{
Sphere.Colour = ((cWell)(CurrentTable.ListTags[IdxPt])).GetClassType().ColourForDisplay;
Sphere.Tag = CurrentTable.ListTags[IdxPt];
}
}
else //if (this.GlobalInfo != null)
{
Sphere.Colour = cGlobalInfo.ListCellularPhenotypes[CurrentSerie % cGlobalInfo.ListCellularPhenotypes.Count].ColourForDisplay;
}
TmpListObjects.AddObject(Sphere);
if ((ValueToBeDisplayed > 0) && (ValueToBeDisplayed < CurrentTable.Count))
{
if (_3DWorld != null)
TmpListObjects.Add(new c3DText(_3DWorld, CurrentTable[ValueToBeDisplayed][IdxPt].ToString("N3"), new cPoint3D(Pt.X + 0.02, Pt.Y + 0.02, Pt.Z + 0.02), Color.White, 0.01));
}
}
ListObjects.AddRange(TmpListObjects);
#region Draw Links
if (IsLinked)
{
cListGeometric3DObject ListLinks = new cListGeometric3DObject( "Links MetaObject");
for (int IdxPt = 1; IdxPt < CurrentTable[0].Count; IdxPt++)
{
cPoint3D Pt1 = null;
cPoint3D Pt0 = null;
if (IsNormalized)
{
Pt1 = new cPoint3D((CurrentTable[0][IdxPt] - MinX) / DeltaX, (CurrentTable[1][IdxPt] - MinY) / DeltaY, (CurrentTable[2][IdxPt] - MinZ) / DeltaZ);
Pt0 = new cPoint3D((CurrentTable[0][IdxPt - 1] - MinX) / DeltaX, (CurrentTable[1][IdxPt - 1] - MinY) / DeltaY, (CurrentTable[2][IdxPt - 1] - MinZ) / DeltaZ);
}
else
{
Pt1 = new cPoint3D(CurrentTable[0][IdxPt], CurrentTable[1][IdxPt] , CurrentTable[2][IdxPt] );
Pt0 = new cPoint3D(CurrentTable[0][IdxPt - 1] , CurrentTable[1][IdxPt - 1] , CurrentTable[2][IdxPt - 1] );
}
// new cPoint3D((CurrentTable[0][IdxPt] - MinX) / DeltaX, (CurrentTable[1][IdxPt] - MinY) / DeltaY, (CurrentTable[2][IdxPt] - MinZ) / DeltaZ);
//cPoint3D Pt0 = new cPoint3D((CurrentTable[0][IdxPt - 1] - MinX) / DeltaX, (CurrentTable[1][IdxPt - 1] - MinY) / DeltaY, (CurrentTable[2][IdxPt - 1] - MinZ) / DeltaZ);
c3DLine Line = new c3DLine(Pt0, Pt1);
Line.SetName("Link ["+(IdxPt-1)+";"+IdxPt+"]");
ListLinks.AddObject(Line);
}
ListObjects.AddRange(ListLinks);
}
#endregion
}
#region Draw Axis
if (IsdrawAxis && (this.Input[0].Count > 2))
{
c3DObject_Axis Axis = new c3DObject_Axis();
cExtendedTable T = new cExtendedTable();
T.Add(new cExtendedList(Input[0][0].Name));
if (IsNormalized)
{
T[0].Tag = Input[0][0].Tag;
T[0].Add(0);
T[0].Add(1);
T.Add(new cExtendedList(Input[0][1].Name));
T[1].Tag = Input[0][1].Tag;
T[1].Add(0);
T[1].Add(1);
T.Add(new cExtendedList(Input[0][2].Name));
T[2].Tag = Input[0][2].Tag;
T[2].Add(0);
T[2].Add(1);
}
else
{
T[0].Tag = Input[0][0].Tag;
T[0].Add(MinX);
T[0].Add(MaxX);
T.Add(new cExtendedList(Input[0][1].Name));
T[1].Tag = Input[0][1].Tag;
T[1].Add(MinY);
T[1].Add(MaxY);
T.Add(new cExtendedList(Input[0][2].Name));
T[2].Tag = Input[0][2].Tag;
T[2].Add(MinZ);
T[2].Add(MaxZ);
}
Axis.SetInputData(T);
Axis.Run(_3DWorld);
ListObjects.AddRange(Axis.GetOutPut());
}
#endregion
// _3DWorld.AddGeometric3DObjects(this.ListObjects);
return base.FeedBackMessage;
}
private void ToolStripMenuItem_Display3DTexture(object sender, EventArgs e)
{
cViewer3D V3D = new cViewer3D();
c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));
cListGeometric3DObject GlobalList = new cListGeometric3DObject("2D Texture Metaobject");
c3DTexturedPlan _3DPlan = new c3DTexturedPlan(new cPoint3D(0, 0, 0), this.AssociatedImage);
// c3DElevationMap _3DMap = new c3DElevationMap(new cPoint3D(0, 0, 0), this.Input, this.LUT);
_3DPlan.SetName("2D Texture");
_3DPlan.Run();
GlobalList.Add(_3DPlan);
foreach (var item in GlobalList)
MyWorld.AddGeometric3DObject(item);
// MyWorld.AddLight(Color.White);
V3D.SetInputData(MyWorld);
V3D.Run();
cDisplayToWindow DTW = new cDisplayToWindow();
DTW.SetInputData(V3D.GetOutPut());
DTW.Title = "2D texture (" + this.AssociatedImage.Name + ")";
DTW.Run();
DTW.Display();
}
void baseInit(c3DNewWorld AssociatedWorld)
{
this.WindowVolumeRenderingOption = new FormForVolumeRenderingOption(this);
//this.WindowVolumeRenderingOption.Visible = false;
this.WindowVolumeRenderingOption.Show();
this.WindowVolumeRenderingOption.Visible = false;
this.AssociatedWorld = AssociatedWorld;
}
private void basic3DToolStripMenuItem_Click(object sender, EventArgs e)
{
cViewer3D V3D = new cViewer3D();
c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));
c3DTexturedPlan Plan = new c3DTexturedPlan(new cPoint3D(0, 0, 0), new cImage(256, 256, 1, 1));
Plan.Run();
MyWorld.AddGeometric3DObject(Plan);
V3D.SetInputData(MyWorld);
V3D.Run();
cDisplayToWindow DTW = new cDisplayToWindow();
DTW.SetInputData(V3D.GetOutPut());
DTW.Run();
DTW.Display();
}
private void dDisplayToolStripMenuItem_Click(object sender, EventArgs e)
{
cViewer3D V3D = new cViewer3D();
c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));
MyWorld.BackGroundColor = cGlobalInfo.OptionsWindow.FFAllOptions.panelFor3DBackColor.BackColor;
V3D.SetInputData(MyWorld);
V3D.Run();
cDesignerSinglePanel CD = new cDesignerSinglePanel();
CD.SetInputData(V3D.GetOutPut());
if (CD.Run().IsSucceed == false) return;
cDisplayToWindow CDW = new cDisplayToWindow();
CDW.SetInputData(CD.GetOutPut());
CDW.Title = "3D world";
if (CDW.Run().IsSucceed == false) return;
CDW.Display();
}
public void SetInputData(c3DNewWorld Input)
{
this.Input = Input;
}
public cFeedBackMessage Run(c3DNewWorld _3DWorld)
{
if (this.Input == null)
{
FeedBackMessage.IsSucceed = false;
FeedBackMessage.Message = "No input data table defined.";
return FeedBackMessage;
}
ListObjects = new cListGeometric3DObject("Axis MetaObject");
cExtendedList ListLenghts = new cExtendedList();
double MinLenght;
cPoint3D Pt1 = null;
cPoint3D Pt2 = null;
cPoint3D Pt3 = null;
if (this.Input.Count == 1)
{
cPoint3D Pt0 = new cPoint3D(this.Input[0][0], 0, 0);
Pt1 = new cPoint3D(this.Input[0][1], 0, 0);
ListLenghts.Add(Pt0.DistTo(Pt1));
MinLenght = ListLenghts.Min();
if (MinLenght == 0) MinLenght = 1;
c3DLine XAxis = new c3DLine(Pt0, Pt1);
XAxis.Tag = this.Input[0].Tag;
XAxis.SetName("Axis - " + this.Input[0].Name);
ListObjects.AddObject(XAxis);
}
else if (this.Input.Count == 2)
{
cPoint3D Pt0 = new cPoint3D(this.Input[0][0], this.Input[1][0], 0);
Pt1 = new cPoint3D(this.Input[0][1], this.Input[1][0], 0);
ListLenghts.Add(Pt0.DistTo(Pt1));
Pt2 = new cPoint3D(this.Input[0][0], this.Input[1][1], 0);
ListLenghts.Add(Pt0.DistTo(Pt2));
MinLenght = ListLenghts.Min();
if (MinLenght == 0) MinLenght = 1;
c3DLine XAxis = new c3DLine(Pt0, Pt1);
XAxis.Tag = this.Input[0].Tag;
XAxis.SetName("Axis - " + this.Input[0].Name);
ListObjects.AddObject(XAxis);
c3DLine YAxis = new c3DLine(Pt0, Pt2);
YAxis.Tag = this.Input[1].Tag;
YAxis.SetName("Axis - " + this.Input[1].Name);
ListObjects.AddObject(YAxis);
}
else
{
cPoint3D Pt0 = new cPoint3D(this.Input[0][0], this.Input[1][0], this.Input[2][0]);
Pt1 = new cPoint3D(this.Input[0][1], this.Input[1][0], this.Input[2][0]);
ListLenghts.Add(Pt0.DistTo(Pt1));
Pt2 = new cPoint3D(this.Input[0][0], this.Input[1][1], this.Input[2][0]);
ListLenghts.Add(Pt0.DistTo(Pt2));
Pt3 = new cPoint3D(this.Input[0][0], this.Input[1][0], this.Input[2][1]);
ListLenghts.Add(Pt0.DistTo(Pt3));
MinLenght = ListLenghts.Min();
if (MinLenght == 0) MinLenght = 1;
c3DLine XAxis = new c3DLine(Pt0, Pt1,Color.Black);
XAxis.Tag = this.Input[0].Tag;
XAxis.SetName("Axis - " + this.Input[0].Name);
ListObjects.AddObject(XAxis);
c3DLine YAxis = new c3DLine(Pt0, Pt2,Color.Black);
YAxis.Tag = this.Input[1].Tag;
YAxis.SetName("Axis - " + this.Input[1].Name);
ListObjects.AddObject(YAxis);
c3DLine ZAxis = new c3DLine(Pt0, Pt3,Color.Black);
ZAxis.Tag = this.Input[2].Tag;
ZAxis.SetName("Axis - " + this.Input[2].Name);
ListObjects.AddObject(ZAxis);
}
#region draw text
double TextScale = MinLenght;
if (MinLenght == 1) TextScale = 1;
cPoint3D PosText = Pt1;
// display the axis name
c3DText TmpText = new c3DText(_3DWorld, this.Input[0].Name, PosText, Color.Black, 0.02 * TextScale);
TmpText.Tag = this.Input[0].Tag;
ListObjects.AddObject(TmpText);
// MinX
PosText = new cPoint3D(0, 0, 0);
PosText.X = this.Input[0][0];
if (this.Input.Count > 1) PosText.Y = this.Input[1][0];
if (this.Input.Count > 2) PosText.Z = this.Input[2][0] - TextScale * 0.03;
ListObjects.AddObject(new c3DText(_3DWorld, this.Input[0][0].ToString("N3"), PosText, Color.DimGray, 0.01 * TextScale));
// MaxX
PosText.X = this.Input[0][1];
if (this.Input.Count > 1) PosText.Y = this.Input[1][0];
if (this.Input.Count > 2) PosText.Z = this.Input[2][0] - TextScale * 0.03;
if (this.Input.Count > 1) ListObjects.AddObject(new c3DText(_3DWorld, this.Input[0][1].ToString("N3"), PosText, Color.DimGray, 0.01 * TextScale));
if (Pt2 != null)
{
PosText = Pt2;
TmpText = new c3DText(_3DWorld, this.Input[1].Name, PosText, Color.Black, 0.02 * TextScale);
TmpText.Tag = this.Input[1].Tag;
ListObjects.AddObject(TmpText);
// MinY
PosText.X = this.Input[0][0] - TextScale * 0.03;// + TextScale*0.02;
if (this.Input.Count > 1) PosText.Y = this.Input[1][0];// -TextScale * 0.03;
if (this.Input.Count > 2) PosText.Z = this.Input[2][0] - TextScale * 0.03;
ListObjects.AddObject(new c3DText(_3DWorld, this.Input[1][0].ToString("N3"), PosText, Color.DimGray, 0.01 * TextScale));
PosText.X = this.Input[0][0] - TextScale * 0.03;// + TextScale*0.02;
if (this.Input.Count > 1) PosText.Y = this.Input[1][1];// -TextScale * 0.03;
if (this.Input.Count > 2) PosText.Z = this.Input[2][0] - TextScale * 0.03;
ListObjects.AddObject(new c3DText(_3DWorld, this.Input[1][1].ToString("N3"), PosText, Color.DimGray, 0.01 * TextScale));
}
if (Pt3 != null)
{
PosText = Pt3;
TmpText = new c3DText(_3DWorld, this.Input[2].Name, /*new cPoint3D(-0.04, -0.04, 0.45)*/ PosText, Color.Black, 0.02 * TextScale);
TmpText.Tag = this.Input[2].Tag;
ListObjects.AddObject(TmpText);
PosText.X = this.Input[0][0] - TextScale * 0.03;// + TextScale*0.02;
PosText.Y = this.Input[1][0];// -TextScale * 0.03;
PosText.Z = this.Input[2][0];
ListObjects.AddObject(new c3DText(_3DWorld, this.Input[2][0].ToString("N3"), PosText, Color.DimGray, 0.01 * TextScale));
PosText.X = this.Input[0][0] - TextScale * 0.03;// + TextScale*0.02;
PosText.Y = this.Input[1][0];// -TextScale * 0.03;
PosText.Z = this.Input[2][1];
ListObjects.AddObject(new c3DText(_3DWorld, this.Input[2][1].ToString("N3"), PosText, Color.DimGray, 0.01 * TextScale));
}
#endregion
return base.FeedBackMessage;
}
private void ToolStripMenuItem_Display3DScatterGraph(object sender, EventArgs e)
{
cExtendedTable CET = new cExtendedTable();
foreach (DataGridViewColumn item in GridView.SelectedColumns)
{
CET.Add(Input[item.Index]);
}
if (this.Input.ListTags != null)
{
CET.ListTags = new List<object>();
foreach (var item in this.Input.ListTags)
{
CET.ListTags.Add(item);
}
}
cListExtendedTable LET = new cListExtendedTable();
LET.Add(CET);
//List<cListWells> ListWells = new List<cListWells>();
//ListWells.Add(cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().ListActiveWells);
cViewer3D V3D = new cViewer3D();
c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));
c3DObjectScatterPoints _3DScatterPt = new c3DObjectScatterPoints();
_3DScatterPt.ListProperties.FindByName("Draw Axis ?").SetNewValue((bool)true);
_3DScatterPt.ListProperties.FindByName("Draw Axis ?").IsGUIforValue = true;
_3DScatterPt.ListProperties.FindByName("Normalized ?").SetNewValue((bool)true);
_3DScatterPt.ListProperties.FindByName("Normalized ?").IsGUIforValue = true;
_3DScatterPt.ListProperties.FindByName("Link Points ?").SetNewValue((bool)false);
_3DScatterPt.ListProperties.FindByName("Link Points ?").IsGUIforValue = true;
//_3DScatterPt.GlobalInfo = cGlobalInfo;
_3DScatterPt.SetInputData(LET);
if (_3DScatterPt.Run(MyWorld).IsSucceed == false) return;
cListGeometric3DObject GlobalList = _3DScatterPt.GetOutPut();
foreach (var item in GlobalList)
{
MyWorld.AddGeometric3DObject(item);
}
V3D.SetInputData(MyWorld);
V3D.Run();
cDisplayToWindow DTW = new cDisplayToWindow();
DTW.SetInputData(V3D.GetOutPut());
DTW.Title = "3D Scatter Graph ("+ this.Input.Name +")";
DTW.Run();
DTW.Display();
}
public cFeedBackMessage Run(c3DNewWorld _3DWorld)
{
if (base.Start() == false)
{
base.FeedBackMessage.IsSucceed = false;
return base.FeedBackMessage;
}
#region Properties Management
object _firstValue = base.ListProperties.FindByName("Thresold");
double Thresold = 0.5;
if (_firstValue == null)
{
base.GenerateError("-Thresold- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
Thresold = (double)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Thresold- cast didn't work");
return base.FeedBackMessage;
}
_firstValue = base.ListProperties.FindByName("Split objects ?");
bool IsSplit = false;
if (_firstValue == null)
{
base.GenerateError("-Split objects ?- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
IsSplit = (bool)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Split objects ?- cast didn't work");
return base.FeedBackMessage;
}
#endregion
ListObjects = new cListGeometric3DObject("");
if (IsSplit == false)
{
c3DMeshObject MyMesh = null;
if (this.VTKInput == null)
{
MyMesh = new c3DMeshObject(this.Input, Thresold);
}
else
{
MyMesh = new c3DMeshObject(this.VTKInput, (int)Thresold);
}
MyMesh.Create(Color.Aqua, this.Pos );
ListObjects.Name = MyMesh.GetName() + " metaobject";
ListObjects.Add(MyMesh);
}
else
{
// ok that's a little bit more complicated now
// first we need to binarize the image
cImageSegmentationThreshold IST = new cImageSegmentationThreshold();
IST.ListProperties.FindByName("Threshold").SetNewValue(Thresold);
cImage SourceImage = new cImage(this.Input, false);
IST.SetInputData(SourceImage);
IST.Run();
// now perform image labeling
cImage BinImage = IST.GetOutPut();
cImage LabeledImage = new cImage(BinImage, false);
ConnectedComponentSet CCS = new ConnectedComponentSet(BinImage,LabeledImage,SourceImage, 0, eConnectivity.THREED_6, 0, float.MaxValue);
Random RD = new Random();
int IdxObj = 1;
// loop over each object
int NumObj = CCS.Count;
ListObjects.Name = "T_" + Thresold + " [" + SourceImage.Name + " Metaobject";
for(int i = 0;i<NumObj;i++)
{
ConnectedVoxels item = CCS[i];
// if (item.Volume <= 1) continue;
List<cPoint3D> ExtremePts = item.GetExtremaPoints();
// crop the labeled image
cImage TmpIm = LabeledImage.Crop(ExtremePts[0], ExtremePts[1]);
// we have to clean the cropped image to prevent any overlapping object to be segmented
for (int Pix = 0; Pix < TmpIm.ImageSize; Pix++)
{
if ((TmpIm.SingleChannelImage[0].Data[Pix] > 0) && (TmpIm.SingleChannelImage[0].Data[Pix] != IdxObj)) TmpIm.SingleChannelImage[0].Data[Pix] = 0;
}
// update the position of the object
cPoint3D NewPos = ExtremePts[0]*SourceImage.Resolution;
c3DMeshObject MyMesh = new c3DMeshObject(TmpIm.SingleChannelImage[0], 0.5);
MyMesh.Create(Color.FromArgb(RD.Next(255), RD.Next(255), RD.Next(255)), NewPos);
MyMesh.SetName(MyMesh.GetName() + "_" + IdxObj);
MyMesh.AssociatedConnectedComponent = item;
ListObjects.AddObject(MyMesh);
IdxObj++;
}
}
return base.FeedBackMessage;
}
public void Refresh3DScreenView()
{
cViewer3D V3D = new cViewer3D();
c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));
V3D.SetInputData(MyWorld);
c3DObject_Screening2D Screening2D = new c3DObject_Screening2D();
Screening2D.SetInputData(cGlobalInfo.CurrentScreening);
Screening2D.Run(MyWorld);
MyWorld.AddGeometric3DObjects(Screening2D.GetOutPut());
// c3DObject_Plate2D Plate2D = new c3DObject_Plate2D();
// Plate2D.SetInputData(this);
// Plate2D.Run(MyWorld);
// MyWorld.AddGeometric3DObjects(Plate2D.GetOutPut());
// MyWorld.BackGroundColor = Color.White;
V3D.Run();
cExtendedControl EXT = V3D.GetOutPut();
cGlobalInfo.WindowHCSAnalyzer.tabPage3DPlatesView.Controls.Clear();
EXT.Width = cGlobalInfo.WindowHCSAnalyzer.tabPage3DPlatesView.Width;
EXT.Height = cGlobalInfo.WindowHCSAnalyzer.tabPage3DPlatesView.Height;
// EXT.Controls[0].Width = cGlobalInfo.WindowHCSAnalyzer.tabPage3DPlatesView.Width;
// EXT.Controls[0].Height = cGlobalInfo.WindowHCSAnalyzer.tabPage3DPlatesView.Height;
cGlobalInfo.WindowHCSAnalyzer.tabPage3DPlatesView.Controls.Add(EXT);
//cDesignerSinglePanel CD = new cDesignerSinglePanel();
//CD.SetInputData(V3D.GetOutPut());
//if (CD.Run().IsSucceed == false) return;
//cDisplayToWindow CDW = new cDisplayToWindow();
//CDW.SetInputData(CD.GetOutPut());
//CDW.Title = "3D world";
//if (CDW.Run().IsSucceed == false) return;
//CDW.Display();
}
private void GenerateGraph()
{
V3D = new cViewer3D();
MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));
cListGeometric3DObject GlobalList = new cListGeometric3DObject("Elevation Map MetaObject");
if(this.Input!=null)
foreach (var item in this.Input)
{
c3DElevationMap _3DMap = new c3DElevationMap(new cPoint3D(-this.Input[0].Count / 2, -this.Input[0][0].Count / 2, 0), item, this.LUT);
_3DMap.SetName("Elevation Map [" + item.Name +"]");
GlobalList.Add(_3DMap);
}
if (this.InputImage != null)
{
for (int i = 0; i < this.InputImage.GetNumChannels(); i++)
{
c3DElevationMap _3DMapFromImage = new c3DElevationMap(new cPoint3D(0, 0, 0), this.InputImage, i, 0);
if(this.InputImage.AssociatedImagePanel!=null)
_3DMapFromImage.SetOpacity(this.InputImage.AssociatedImagePanel.LUTManager.GetImageDisplayProperties().ListOpacity[i]/100.0);
_3DMapFromImage.SetName("Elevation Map [" + this.InputImage.SingleChannelImage[i].Name+"]");
GlobalList.Add(_3DMapFromImage);
}
}
foreach (var item in GlobalList)
{
MyWorld.AddGeometric3DObject(item);
}
MyWorld.BackGroundColor = cGlobalInfo.OptionsWindow.FFAllOptions.panelFor3DBackColor.BackColor;
V3D.SetInputData(MyWorld);
V3D.Run();
#region obsolete
//// get a reference to the renderwindow of our renderWindowControl1
//vtkRenderWindow RenderWindow = renderWindowControl1.RenderWindow;
//// get a reference to the renderer
//vtkRenderer Renderer = RenderWindow.GetRenderers().GetFirstRenderer();
//vtkPoints points = vtkPoints.New();
//double MaxZ = this.Input.Max();
//double MinZ = this.Input.Min();
//for (int IdxX = 0; IdxX < this.Input.Count; IdxX++)
// for (int IdxY = 0; IdxY < this.Input[IdxX].Count; IdxY++)
// {
// double Value = ((this.Input[IdxX][this.Input[IdxX].Count- IdxY-1] - MinZ) / (MaxZ - MinZ) * this.Input.Count) / 5;
// points.InsertNextPoint(IdxX, IdxY, Value);
// }
//double[] bounds = points.GetBounds();
//// Add the grid points to a polydata object
//vtkPolyData inputPolyData = vtkPolyData.New();
//inputPolyData.SetPoints(points);
//// Triangulate the grid points
//vtkDelaunay2D delaunay = vtkDelaunay2D.New();
//delaunay.SetInput(inputPolyData);
//delaunay.Update();
//vtkElevationFilter elevationFilter = vtkElevationFilter.New();
//elevationFilter.SetInputConnection(delaunay.GetOutputPort());
//elevationFilter.SetLowPoint(0.0, 0.0, bounds[5]);
//elevationFilter.SetHighPoint(0.0, 0.0, bounds[4]);
//elevationFilter.Update();
//vtkPolyData output = vtkPolyData.New();
//output.ShallowCopy(vtkPolyData.SafeDownCast(elevationFilter.GetOutput()));
//// Generate the colors for each point based on the color map
//vtkUnsignedCharArray colors = vtkUnsignedCharArray.New();
//colors.SetNumberOfComponents(3);
//colors.SetName("Colors");
//output.GetPointData().AddArray(colors);
//// Visualize
//vtkPolyDataMapper mapper = vtkPolyDataMapper.New();
//mapper.SetInput(output);
//// Create the color map
//vtkLookupTable colorLookupTable = vtkLookupTable.New();
//colorLookupTable.Build();
//if (LUT == null)
//{
// cLUT MyLut = new cLUT();
// LUT = MyLut.LUT_JET;
//}
////colorLookupTable.SetValueRange(1,0);//bounds[0], bounds[1]);
//double LUTSize = LUT[0].Length;
//colorLookupTable.SetNumberOfTableValues((int)LUTSize - 1);
//for (int i = 0; i < (int)LUTSize - 1; i++)
//{
// colorLookupTable.SetTableValue((int)LUTSize - 1 - i-1, this.LUT[0][i] / LUTSize, this.LUT[1][i] / LUTSize, this.LUT[2][i] / LUTSize, 1);
//}
////colorLookupTable.SetSaturationRange(0, 0);
////colorLookupTable.SetTableRange(bounds[4], bounds[5]);
////table.SetRange(range[0], range[1]); //shoul here not be the minimum/maximum possible of "data"?
//// colorLookupTable.SetRampToLinear();
//colorLookupTable.Build();
//mapper.SetLookupTable(colorLookupTable);
//vtkActor NewActor = vtkActor.New();
//NewActor.SetMapper(mapper);
//Renderer.AddActor(NewActor);
//// set background color
//Renderer.SetBackground(BackGroundColor.R / 255.0, BackGroundColor.G / 255.0, BackGroundColor.B / 255.0);
//// ensure all actors are visible (in this example not necessarely needed,
//// but in case more than one actor needs to be shown it might be a good idea)
//Renderer.ResetCamera();
#endregion
}
public cVolumeRendering3D(cSingleChannelImage SingleChannelImage, cPoint3D Pos, byte[][] NewLUT, c3DNewWorld AssociatedWorld)
{
if (SingleChannelImage.Data == null) return;
baseInit(AssociatedWorld);
this.SetName("Volume 3D [" + SingleChannelImage.Name + "]");
this.LUT = NewLUT;
vtk_volume = vtkVolume.New();
vtkImageData imageData = vtkImageData.New();
vtkUnsignedShortArray UshortArray = vtkUnsignedShortArray.New();
voi = vtkExtractVOI.New();
ColorTransferFunction = vtkColorTransferFunction.New();
for (int i = 0; i < SingleChannelImage.Width * SingleChannelImage.Height * SingleChannelImage.Depth; i++)
{
UshortArray.InsertTuple1(i, (ushort)SingleChannelImage.Data[i]); // data are converted to UShort
}
imageData = vtkImageData.New();
imageData.SetDimensions(SingleChannelImage.Width, SingleChannelImage.Height, SingleChannelImage.Depth);
imageData.SetOrigin(0, 0, 0);
if ((SingleChannelImage.Resolution.X == 0) || (SingleChannelImage.Resolution.Y == 0) || (SingleChannelImage.Resolution.Z == 0))
imageData.SetSpacing(1.0, 1.0, 1.0);
else
imageData.SetSpacing(SingleChannelImage.Resolution.X, SingleChannelImage.Resolution.Y, SingleChannelImage.Resolution.Z);
imageData.GetPointData().SetScalars(UshortArray);
voi = vtkExtractVOI.New();
voi.SetInput(imageData);
voi.SetVOI(0, SingleChannelImage.Width - 1, 0, SingleChannelImage.Height - 1, 0, SingleChannelImage.Depth - 1);
voi.SetSampleRate(1, 1, 1);
opacityTransferFunction = vtkPiecewiseFunction.New();
range = imageData.GetScalarRange();
opacityTransferFunction.AddPoint(range[0], 0.0);
opacityTransferFunction.AddPoint(range[1], 0.3);
//opacityTransferFunction.AddPoint(2000, 0.1);
//opacityTransferFunction.AddPoint(range[0] + (range[1]-range[0])/2.0, 0.0);
//opacityTransferFunction.AddPoint(range[1], 0.7);
if (LUT == null)
{
//cLUT MyLut = new cLUT();
//LUT = MyLut.LUT_JET;
ColorTransferFunction.AddRGBPoint(0, 0 , 0, 0);
ColorTransferFunction.AddRGBPoint(1, 1, 1, 1);
}
//double LUTSize = LUT[0].Length;
//for (int i = 0; i < (int)LUTSize; i++)
//{
// colorTransferFunction.AddRGBPoint(i, LUT[0][i] / LUTSize, LUT[1][i] / LUTSize, LUT[2][i] / LUTSize);
//}
ColorTransferFunction.Build();
volumeProperty = vtkVolumeProperty.New();
volumeProperty.SetColor(ColorTransferFunction);
volumeProperty.SetScalarOpacity(opacityTransferFunction);
volumeProperty.SetInterpolationTypeToNearest();
volumeProperty.ShadeOff();
vtkVolumeTextureMapper3D volumeTextureMapper = vtkVolumeTextureMapper3D.New();
volumeTextureMapper.SetInputConnection(voi.GetOutputPort());
//vtkVolumeRayCastCompositeFunction compositeFunction = vtkVolumeRayCastCompositeFunction.New();
//vtkVolumeRayCastMapper volumeMapper = vtkVolumeRayCastMapper.New();
//volumeMapper.SetVolumeRayCastFunction(compositeFunction);
//volumeMapper.SetInputConnection(voi.GetOutputPort());
vtk_volume = vtkVolume.New();
vtk_volume.SetMapper(volumeTextureMapper);
vtk_volume.SetProperty(volumeProperty);
vtk_volume.PickableOn();
vtk_volume.SetPosition(Pos.X, Pos.Y, Pos.Z);
}
private void dRC3DToolStripMenuItem_Click(object sender, EventArgs e)
{
if (cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptors().Count < 3)
{
MessageBox.Show("At least 3 descriptors are required for this operation !", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
cListExtendedTable LET = new cListExtendedTable();
//List<cListWells> ListWells = new List<cListWells>();
//ListWells.Add(cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().ListActiveWells);
// firstly, wells are grouped by class
//foreach (var item in cGlobalInfo.ListWellClasses)
//{
// List<cWellClassType> TypeForFilter = new List<cWellClassType>();
// TypeForFilter.Add(item);
// cListWells TmpListWells = cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().ListActiveWells.Filter(TypeForFilter);
// cGeneralDRC gDRC = new cGeneralDRC(TmpListWells);
// LET.Add(gDRC.ListAverageValues);
//}
for (int i = 0; i < 3; i++)
{
List<int> GroupForFilter = new List<int>();
GroupForFilter.Add(i);
cListWells TmpListWells = cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().ListActiveWells.FilterByGroup(GroupForFilter);
cGeneralDRC gDRC = new cGeneralDRC(TmpListWells);
LET.Add(gDRC.ListAverageValues);
}
cViewer3D V3D = new cViewer3D();
c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));
c3DObjectScatterPoints _3DScatterPt = new c3DObjectScatterPoints();
//_3DScatterPt.SetInputData(cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().ListActiveWells.GetDescriptorValues(cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptors(), false));
// _3DScatterPt.GlobalInfo = this.GlobalInfo;
_3DScatterPt.SetInputData(LET);
// _3DScatterPt.IsLinked = true;
_3DScatterPt.Run(MyWorld);
cListGeometric3DObject GlobalList = _3DScatterPt.GetOutPut();
foreach (var item in GlobalList)
{
MyWorld.AddGeometric3DObject(item);
}
MyWorld.BackGroundColor = cGlobalInfo.OptionsWindow.FFAllOptions.panelFor3DBackColor.BackColor;
V3D.SetInputData(MyWorld);
V3D.Run();
cDisplayToWindow DTW = new cDisplayToWindow();
DTW.SetInputData(V3D.GetOutPut());
DTW.Title = "3D Dose Response Visualization";
DTW.Run();
DTW.Display();
}
private void dToolStripMenuItemScatterPlot3D_Click(object sender, EventArgs e)
{
int MaxNumberOfPts = (int)cGlobalInfo.OptionsWindow.FFAllOptions.numericUpDownMinNumPointForFastDisp.Value;
if (cGlobalInfo.CurrentScreening.ListPlatesActive.GetListActiveWells().Count > MaxNumberOfPts)
{
cExtendedTable ET = cGlobalInfo.CurrentScreening.ListPlatesActive.GetListActiveWells().GetAverageDescriptorValues(cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptors(), false, false);
cNormalize N = new cNormalize();
N.SetInputData(ET);
N.NormalizationType = eNormalizationType.MIN_MAX;
N.Run();
cExtendedTable NormTable = N.GetOutPut();
cViewer3D V3D = new cViewer3D();
c3DPointCloud _3DPtCloud = new c3DPointCloud(NormTable);
_3DPtCloud.AutomatedPtColorMode = 1;
_3DPtCloud.Create(new cPoint3D(0, 0, 0));
_3DPtCloud.SetName("_3DPtCloud");
cListGeometric3DObject GlobalList = new cListGeometric3DObject("3D Point Cloud MetaObject");
GlobalList.Add(_3DPtCloud);
c3DObject_Axis Axis = new c3DObject_Axis();
cExtendedTable T = new cExtendedTable();
T.Add(new cExtendedList(ET[0].Name));
T[0].Tag = ET[0].Tag;
T[0].Add(0);
T[0].Add(1);
T.Add(new cExtendedList(ET[1].Name));
T[1].Tag = ET[1].Tag;
T[1].Add(0);
T[1].Add(1);
if (ET.Count > 2)
{
T.Add(new cExtendedList(ET[2].Name));
T[2].Tag = ET[2].Tag;
T[2].Add(0);
T[2].Add(1);
}
Axis.SetInputData(T);
c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));
Axis.Run(MyWorld);
GlobalList.AddRange(Axis.GetOutPut());
// GlobalList.Add(Axis);
foreach (var item in GlobalList)
{
MyWorld.AddGeometric3DObject(item);
}
// MyWorld.BackGroundColor = cGlobalInfo.OptionsWindow.FFAllOptions.panelFor3DBackColor.BackColor;
V3D.SetInputData(MyWorld);
V3D.Run();
cDisplayToWindow DTW = new cDisplayToWindow();
DTW.SetInputData(V3D.GetOutPut());
DTW.Title = "3D Cloud Point - " + ET[0].Count + " points";
DTW.Run();
DTW.Display();
}
else
{
cGlobalInfo.OptionsWindow.checkBoxConnectDRCPts.Checked = false;
FormFor3DDataDisplay FormToDisplayXYZ = new FormFor3DDataDisplay(ProcessModeEntireScreeningToolStripMenuItem.Checked, cGlobalInfo.CurrentScreening);
for (int i = 0; i < (int)cGlobalInfo.CurrentScreening.ListDescriptors.Count; i++)
{
FormToDisplayXYZ.comboBoxDescriptorX.Items.Add(cGlobalInfo.CurrentScreening.ListDescriptors[i].GetName());
FormToDisplayXYZ.comboBoxDescriptorY.Items.Add(cGlobalInfo.CurrentScreening.ListDescriptors[i].GetName());
FormToDisplayXYZ.comboBoxDescriptorZ.Items.Add(cGlobalInfo.CurrentScreening.ListDescriptors[i].GetName());
}
FormToDisplayXYZ.Show();
FormToDisplayXYZ.comboBoxDescriptorX.Text = cGlobalInfo.CurrentScreening.ListDescriptors[0].GetName() + " ";
FormToDisplayXYZ.comboBoxDescriptorY.Text = cGlobalInfo.CurrentScreening.ListDescriptors[0].GetName() + " ";
FormToDisplayXYZ.comboBoxDescriptorZ.Text = cGlobalInfo.CurrentScreening.ListDescriptors[0].GetName() + " ";
}
return;
}
void renderWindowControl1_Disposed(object sender, EventArgs e)
{
this.Input.Dispose();
this.Input = null;
GC.SuppressFinalize(this);
GC.Collect();
}
private void spiralToolStripMenuItem_Click(object sender, EventArgs e)
{
// first let's define all the stimuli
#region Build the stimuli
cStimuli ListCellStimuli = new cStimuli();
cStimulus_Physical Gravity = new cStimulus_Physical("Gravity");
ListCellStimuli.Add(Gravity);
//cStimulus_Physical WorldEdges = new cStimulus_Physical("World Edges");
//ListCellStimuli.Add(WorldEdges);
cStimulus_Physical BrownianMotion = new cStimulus_Physical("Brownian Motion");
ListCellStimuli.Add(BrownianMotion);
cStimulus_Chemical ToxicCompound1 = new cStimulus_Chemical("ToxicCompound1");
ListCellStimuli.Add(ToxicCompound1);
#endregion
#region build the cell agents
#endregion
cNewAgent BiologicalExperiment_DRC = new cNewAgent(new cPoint3D(0, 0, 0), new cPoint3D(5, 5, 5), "DRC");
double Concentration = 0.01;
for (int i = 0; i < 2; i++)
{
double WellSpacing = 1;
cNewAgent BiologicalExperiment_Well = new cNewAgent(new cPoint3D(WellSpacing, 0, 0), new cPoint3D(1, 1, 1), "Well " + i);
// add a new Property to the well
cInternalProperty Cpd1Concentration = new cInternalProperty();
Cpd1Concentration.Name = "Compound 1 Concentration";
BiologicalExperiment_Well.AddProperty(Cpd1Concentration);
// add the cellular agents in the well
int RegularCellsNumber = 20;
for (int CellIdx = 0; CellIdx < RegularCellsNumber; CellIdx++)
{
cAgent_Cell Agent_RegularCell = new cAgent_Cell(new cPoint3D(0.02 * CellIdx, 0.2, 0.0200 * i), new cPoint3D(0.0100, 0.0100, 0.0100), "Regular Cell " + CellIdx);
Agent_RegularCell.AssociatedStimuli = ListCellStimuli;
BiologicalExperiment_Well.AddNewAgent(Agent_RegularCell);
}
int CancerCellsNumber = 30;
for (int CellIdx = 0; CellIdx < CancerCellsNumber; CellIdx++)
{
cAgent_Cell Agent_CancerCell = new cAgent_Cell(new cPoint3D(0.0100 * i, 0.0100 * CellIdx, 0.1000), new cPoint3D(0.0200, 0.0200, 0.0200), "Cancer Cell " + CellIdx);
Agent_CancerCell.AssociatedStimuli = ListCellStimuli;
BiologicalExperiment_Well.AddNewAgent(Agent_CancerCell);
}
// add the well agent in the DRC
BiologicalExperiment_DRC.AddNewAgent(BiologicalExperiment_Well);
Concentration *= 2;
}
for (int Iteration = 0; Iteration < 1; Iteration++)
{
BiologicalExperiment_DRC.Run();
}
// display objects in 3D
cViewer3D V3D = new cViewer3D();
// c3DNewWorld MyWorld = new c3DNewWorld((cPoint3D)BiologicalExperiment_DRC.InternalProperties["Volume"], new cPoint3D(1, 1, 1));
c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));
V3D.SetInputData(MyWorld);
V3D.Run();
cDesignerSinglePanel CD = new cDesignerSinglePanel();
CD.SetInputData(V3D.GetOutPut());
if (CD.Run().IsSucceed == false) return;
cListGeometric3DObject GlobalList = new cListGeometric3DObject("Global List");
cListGeometric3DObject CellsList = new cListGeometric3DObject("Cells");
cInternalProperty TmpProp;
foreach (cNewAgent TmpWell in BiologicalExperiment_DRC)
{
cPoint3D ObjectPos = TmpWell.GetAbsoluteGetPosition();
c3DCube SpaceCube = new c3DCube();
TmpProp = TmpWell.InternalProperties["Volume"];
cPoint3D VOlume = new cPoint3D(0, 0, 0);
SpaceCube.Create(ObjectPos, VOlume, Color.Blue);
SpaceCube.SetOpacity(0.2);
GlobalList.AddObject(SpaceCube);
foreach (cNewAgent TmpCell in TmpWell)
{
ObjectPos = TmpCell.GetAbsoluteGetPosition();
c3DSphere _3DSphere = new c3DSphere(ObjectPos, 0.05, Color.Red);
TmpProp = TmpCell.InternalProperties["Volume"];
VOlume = new cPoint3D(0, 0, 0);// (cPoint3D)TmpCell.InternalProperties["Volume"];
//_3DSphere.(ObjectPos, 0.5, Color.Red);
_3DSphere.SetName(TmpCell.GetName());
_3DSphere.SetOpacity(1);
CellsList.AddObject(_3DSphere);
}
}
GlobalList.AddRange(CellsList);
foreach (var item in GlobalList)
MyWorld.AddGeometric3DObject(item);
cDisplayToWindow CDW = new cDisplayToWindow();
CDW.SetInputData(CD.GetOutPut());
CDW.Title = "3D world";
if (CDW.Run().IsSucceed == false) return;
CDW.Display();
return;
}
public cFeedBackMessage Run()
{
if (base.Start() == false)
{
base.FeedBackMessage.IsSucceed = false;
return base.FeedBackMessage;
}
if ((this.Input == null)||(this.Input.Count==0))
{
FeedBackMessage.IsSucceed = false;
FeedBackMessage.Message = "No input data defined.";
return FeedBackMessage;
}
FeedBackMessage.IsSucceed = true;
#region Properties Management
object _firstValue = base.ListProperties.FindByName("Normalized ?");
bool IsNormalized = false;
if (_firstValue == null)
{
base.GenerateError("-Normalized ?- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
IsNormalized = (bool)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Normalized ?- cast didn't work");
return base.FeedBackMessage;
}
_firstValue = base.ListProperties.FindByName("Draw Axis ?");
bool IsdrawAxis = true;
if (_firstValue == null)
{
base.GenerateError("-Draw Axis ?- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
IsdrawAxis = (bool)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Draw Axis ?- cast didn't work");
return base.FeedBackMessage;
}
_firstValue = base.ListProperties.FindByName("Link Points ?");
bool IsLinked = false;
if (_firstValue == null)
{
base.GenerateError("-Link Points ?- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
IsLinked = (bool)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Link Points ?- cast didn't work");
return base.FeedBackMessage;
}
_firstValue = base.ListProperties.FindByName("Desc. 1");
string Desc1;
if (_firstValue == null)
{
base.GenerateError("-Desc. 1- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
Desc1 = (string)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Desc. 1- cast didn't work");
return base.FeedBackMessage;
}
cDescriptorType DescX = cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorByName(Desc1);
if (DescX == null)
{
base.GenerateError(Desc1 + " is not a descriptor !");
return base.FeedBackMessage;
}
_firstValue = base.ListProperties.FindByName("Desc. 2");
if (_firstValue == null)
{
base.GenerateError("-Desc. 2- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
Desc1 = (string)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Desc. 2- cast didn't work");
return base.FeedBackMessage;
}
cDescriptorType DescY = cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorByName(Desc1);
if (DescY == null)
{
base.GenerateError(Desc1 + " is not a descriptor !");
return base.FeedBackMessage;
}
_firstValue = base.ListProperties.FindByName("Desc. 3");
if (_firstValue == null)
{
base.GenerateError("-Desc. 3- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
Desc1 = (string)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Desc. 2- cast didn't work");
return base.FeedBackMessage;
}
cDescriptorType DescZ = cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorByName(Desc1);
if (DescZ == null)
{
base.GenerateError(Desc1 + " is not a descriptor !");
return base.FeedBackMessage;
}
#endregion
List<cDescriptorType> ListDesc = new List<cDescriptorType>();
ListDesc.Add(DescX);
ListDesc.Add(DescY);
ListDesc.Add(DescZ);
cListExtendedTable LET = new cListExtendedTable();
foreach (var item in cGlobalInfo.ListWellClasses)
{
List<cWellClassType> TypeForFilter = new List<cWellClassType>();
TypeForFilter.Add(item);
cExtendedTable TmpTable = ((cListWells)this.Input.Filter(TypeForFilter)).GetAverageDescriptorValues(ListDesc,false, false);
if (TmpTable != null)
LET.Add(TmpTable);
}
cViewer3D V3D = new cViewer3D();
c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));
c3DObjectScatterPoints _3DScatterPt = new c3DObjectScatterPoints();
_3DScatterPt.ListProperties.FindByName("Draw Axis ?").SetNewValue(IsdrawAxis);
_3DScatterPt.ListProperties.FindByName("Normalized ?").SetNewValue(IsNormalized);
_3DScatterPt.ListProperties.FindByName("Link Points ?").SetNewValue(IsLinked);
_3DScatterPt.SetInputData(LET);
if (_3DScatterPt.Run(MyWorld).IsSucceed == false) return base.FeedBackMessage;
cListGeometric3DObject GlobalList = _3DScatterPt.GetOutPut();
foreach (var item in GlobalList)
{
MyWorld.AddGeometric3DObject(item);
}
MyWorld.BackGroundColor = cGlobalInfo.OptionsWindow.FFAllOptions.panelFor3DBackColor.BackColor;
V3D.SetInputData(MyWorld);
V3D.Run();
cDisplayToWindow DTW = new cDisplayToWindow();
DTW.SetInputData(V3D.GetOutPut());
DTW.Title = "3D Scatter Plot(List "+this.Input.Count +" Wells)";
DTW.Run();
DTW.Display();
return base.FeedBackMessage;
}
private void AnalyseSequence(cImage SeqToAnalyse)
{
// //FormForThumbnails WindThumbnail = new FormForThumbnails();
// //for (int k = 0; k < ListFormForControl.Count; k++)
// //{
// // FormForControl Obj = ListFormForControl.ElementAt(ListFormForControl.Count - k-1);
// // Obj.DisplayThumbnail(WindThumbnail);
// //}
// //WindThumbnail.Show();
// //return;
#region initialization
if (SeqToAnalyse == null) return;
// create World
if (Current3DWorld == null)
{
Current3DWorld = new c3DNewWorld(new cPoint3D(SeqToAnalyse.Width, SeqToAnalyse.Height, SeqToAnalyse.Depth),
new cPoint3D(SeqToAnalyse.Resolution));
}
else
{
// // Current3DWorld.ren1.
// Current3DWorld.Terminate();
Current3DWorld = null;
Current3DWorld = new c3DNewWorld(new cPoint3D(SeqToAnalyse.Width, SeqToAnalyse.Height, SeqToAnalyse.Depth),
new cPoint3D(SeqToAnalyse.Resolution));
}
for (int k = 0; k < ListFormForControl.Count; k++)
{
FormForControl Obj = ListFormForControl.ElementAt(ListFormForControl.Count - k-1);
if (Obj.numericUpDownChannel.Value >= SeqToAnalyse.GetNumChannels())
{
MessageBox.Show("Wrong number of channels", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
}
// // Current3DWorld.ListObjControl = ListFormForControl;
// // dataGridViewForClassif.DataSource = CurrentTable;
// if (DataGrid == null)
// {
// DataGrid = new FormForDataGridView();
// DataGrid.Show();
// }
// Current3DWorld.SetLinkToDataGridView(DataGrid.dataGridViewForResults);
Current3DWorld.ListMetaObjectList = new List<cMetaBiologicalObjectList>();
cMetaBiologicalObjectList ListMetacells = new cMetaBiologicalObjectList("List Meta Objects");
Current3DWorld.ListMetaObjectList.Add(ListMetacells);
#endregion
#region Detection
for (int k = 0; k < ListFormForControl.Count; k++)
{
FormForControl Obj = ListFormForControl.ElementAt(ListFormForControl.Count - k -1);
if (Obj.radioButtonIsVolume.Checked) // we have to detect a volume !
{
cVolumeDetection Detection = new cVolumeDetection(SeqToAnalyse, (int)Obj.numericUpDownChannel.Value, Obj.WindowForVolumeDetection.checkBoxIsBorderKill.Checked);
Detection.SetShift(new cPoint3D((float)Obj.WindowForPreProcessing.numericUpDownShiftX.Value, (float)Obj.WindowForPreProcessing.numericUpDownShiftY.Value, (float)Obj.WindowForPreProcessing.numericUpDownShiftZ.Value));
if ((Obj.checkBoxPreProcessings.Checked == false) || (Obj.WindowForPreProcessing.checkBoxMedianIsDisabled.Checked))
{
Detection.SetMedian(-1);
Detection.SetShift(new cPoint3D(0, 0, 0));
}
else
{
Detection.SetMedian((int)Obj.WindowForPreProcessing.numericUpDownMedianKernel.Value);
Detection.SetShift(new cPoint3D((float)Obj.WindowForPreProcessing.numericUpDownShiftX.Value, (float)Obj.WindowForPreProcessing.numericUpDownShiftY.Value, (float)Obj.WindowForPreProcessing.numericUpDownShiftZ.Value));
}
if (Obj.WindowForVolumeDetection.checkBoxVolumeSmooth.Checked)
Detection.MeshSmoother = new cMeshSmoother((int)Obj.WindowForVolumeDetection.numericUpDownSmoothIterations.Value);
if ((Obj.comboBoxContainer.SelectedItem !=null) && (Obj.comboBoxContainer.SelectedItem.ToString() != ""))
{
Detection.SetContainers(Current3DWorld.GetListBiologicalObjectsOfType(Obj.comboBoxContainer.Items[0].ToString()));
if (Obj.InOrOut.radioButtonIn.Checked) Detection.SetContainersMode(0);
else Detection.SetContainersMode(1);
}
else
Detection.SetContainers(null);
if (Obj.WindowForVolumeDetection.checkBoxIsRegionGrowing.Checked == false) // no region growing direct detection
{
Obj.AssociatedBiologicalObjectList = Detection.IntensityThreshold((float)Obj.WindowForVolumeDetection.numericUpDownIntensityThreshold.Value,
(float)Obj.WindowForVolumeDetection.numericUpDownVolumeMinVol.Value,
(float)Obj.WindowForVolumeDetection.numericUpDownVolumeMaxVol.Value);
}
else // region growing
{
if (Obj.WindowForVolumeDetection.radioButtonRegionsBased.Checked) // start from a segmentation
{
if (Obj.WindowForVolumeDetection.radioButtonVolumeDetectionNew.Checked) // a new segmentation has to be performed
{
// // Image3D CurrentPatch = new Image3D(2 * Radius, 2 * Radius, 1, CurrentImageToProcess.NumBands);
cImage CurrentBinary = new cImage(SeqToAnalyse.Width, SeqToAnalyse.Height, SeqToAnalyse.Depth, 1);
for (int i = 0; i < CurrentBinary.ImageSize; i++)
{
if (SeqToAnalyse.SingleChannelImage[(int)Obj.numericUpDownChannel.Value].Data[i] >= (float)Obj.WindowForVolumeDetection.numericUpDownIntensityThreshold.Value)
CurrentBinary.SingleChannelImage[0].Data[i] = 1;
}
eConnectivity CurrentConnectivity = eConnectivity.TWOD_4;
if (CurrentBinary.Depth > 1)
CurrentConnectivity = eConnectivity.THREED_6;
ConnectedComponentSet OFNucleus = new ConnectedComponentSet(CurrentBinary, null, null, 0, CurrentConnectivity, (int)Obj.WindowForVolumeDetection.numericUpDownRegionBasedMinArea.Value, (int)Obj.WindowForVolumeDetection.numericUpDownRegionBasedMaxArea.Value);
// // RegionGrowing = new cRegionGrowing(OFNucleus, NewSeq[0], (int)numericUpDownChannelForRegionGrowing.Value, (float)numericUpDownIntensityForRegionGrowing.Value, (int)numericUpDownMaxNucleusArea.Value);
int NumIterations = -1;
if (Obj.WindowForVolumeDetection.checkBoxIsConvergence.Checked == false) NumIterations = (int)Obj.WindowForVolumeDetection.numericUpDownIterationNumber.Value;
float MergingRatio = (float)((Obj.WindowForVolumeDetection.trackBarMergingStrength.Maximum - Obj.WindowForVolumeDetection.trackBarMergingStrength.Value) / 100.0);
Obj.AssociatedBiologicalObjectList = Detection.RegionGrowing(OFNucleus,
(float)Obj.WindowForVolumeDetection.numericUpDownIntensityForRegionGrowing.Value,
(float)Obj.WindowForVolumeDetection.numericUpDownVolumeMinVol.Value,
(float)Obj.WindowForVolumeDetection.numericUpDownVolumeMaxVol.Value, NumIterations, MergingRatio);
}
// else
// {
// throw new System.ArgumentException("Not implemented", "Error");
// }
// }
// else // start from seeds points
// {
// // first gather the seeds
// if (Obj.WindowForVolumeDetection.comboBoxExistingSpotsDetected.Items.Count == 0) break;
// List<cBiological3DObject> ListSeeds = Current3DWorld.GetListBiologicalObjectsOfType(Obj.WindowForVolumeDetection.comboBoxExistingSpotsDetected.Items[0].ToString());
// int NumIterations = -1;
// if (Obj.WindowForVolumeDetection.checkBoxIsConvergence.Checked == false) NumIterations = (int)Obj.WindowForVolumeDetection.numericUpDownIterationNumber.Value;
// float MergingRatio = (float)((Obj.WindowForVolumeDetection.trackBarMergingStrength.Maximum - Obj.WindowForVolumeDetection.trackBarMergingStrength.Value) / 100.0);
// Obj.AssociatedBiologicalObjectList = Detection.RegionGrowing(ListSeeds,
// (float)Obj.WindowForVolumeDetection.numericUpDownIntensityForRegionGrowing.Value,
// (float)Obj.WindowForVolumeDetection.numericUpDownVolumeMinVol.Value,
// (float)Obj.WindowForVolumeDetection.numericUpDownVolumeMaxVol.Value, NumIterations, MergingRatio);
}
}
if (Obj.AssociatedBiologicalObjectList != null)
{
Obj.richTextBoxInfo.AppendText(Obj.AssociatedBiologicalObjectList.Count + " objects detected.");
for (int i = 0; i < Obj.AssociatedBiologicalObjectList.Count; i++)
{
cBiological3DVolume TmpVol = (cBiological3DVolume)Obj.AssociatedBiologicalObjectList[i];
Obj.AssociatedBiologicalObjectList[i].SetType(Obj.textBoxName.Text);
// TmpVol.ThumbnailnewImage = imageListForThumbnail.Images[Obj.AssociatedBiologicalObjectList[i].GetType() + ".jpg"];
Obj.AssociatedBiologicalObjectList[i].Name = Obj.textBoxName.Text + " " + i;
// Obj.AssociatedBiologicalObjectList[i].IsMaster = Obj.IsMasterObject();
// List<double> Res = TmpVol.Information.GetInformation();
if (Obj.checkBoxIsDisplayName.Checked)
{
cGeometric3DObject AssociatedText = TmpVol.AttachText(TmpVol.Name, 10, Color.White);
AssociatedText.IsStayInFrontOfCamera = true;
Current3DWorld.AddGeometric3DObject(AssociatedText);
// TmpVol.AddText(TmpVol.Name, Current3DWorld, (double)Obj.ForText.numericUpDownArrowScale.Value, Obj.ForText.buttonChangeColorPositive.BackColor);
}
if (Obj.checkIsBoxPointingArrow.Checked)
{
cGeometric3DObject AssociatedArrow = TmpVol.AttachPointingArrow((double)Obj.ForArrow.numericUpDownArrowScale.Value,
Obj.ForArrow.buttonChangeColorPositive.BackColor);
Current3DWorld.AddGeometric3DObject(AssociatedArrow);
}
Obj.AssociatedBiologicalObjectList[i].SetOpacity((double)Obj.ColorOpacity.numericUpDownValue.Value);
// if the object it the Master then create a meta-object and put it inside
if (Obj.IsMasterObject())
{
cMetaBiologicalObject Cell = new cMetaBiologicalObject(Obj.WindowForMaster.textBoxName.Text + i, Current3DWorld.ListMetaObjectList[0], Obj.AssociatedBiologicalObjectList[i]);
// // Cell.AddObject(Obj.AssociatedBiologicalObjectList[i]);
Current3DWorld.ListMetaObjectList[0].Add(Cell);
}
}
if (Obj.radioButtonColorSingle.Checked)
Current3DWorld.AddBiological3DObjects(Obj.AssociatedBiologicalObjectList, Obj.buttonChangeColorPositive.BackColor, eColorMode.Regular);
else if (Obj.radioButtonColorRandom.Checked)
Current3DWorld.AddBiological3DObjects(Obj.AssociatedBiologicalObjectList, Obj.buttonChangeColorPositive.BackColor, eColorMode.Random);
else if (Obj.radioButtonColorIndexed.Checked)
Current3DWorld.AddBiological3DObjects(Obj.AssociatedBiologicalObjectList, Obj.buttonChangeColorPositive.BackColor, eColorMode.Indexed);
}
}
else if (Obj.RadioButtonIsSpot.Checked)
{
cSpotDetection Detection = new cSpotDetection(SeqToAnalyse, (int)Obj.numericUpDownChannel.Value);
if ((Obj.checkBoxPreProcessings.Checked == false) || (Obj.WindowForPreProcessing.checkBoxMedianIsDisabled.Checked))
{
Detection.SetMedian(-1);
Detection.SetShift(new cPoint3D(0, 0, 0));
}
else
{
Detection.SetMedian((int)Obj.WindowForPreProcessing.numericUpDownMedianKernel.Value);
Detection.SetShift(new cPoint3D((float)Obj.WindowForPreProcessing.numericUpDownShiftX.Value, (float)Obj.WindowForPreProcessing.numericUpDownShiftY.Value, (float)Obj.WindowForPreProcessing.numericUpDownShiftZ.Value));
}
if ((Obj.comboBoxContainer.Items.Count > 0) && (Obj.comboBoxContainer.SelectedItem != null))
{
Detection.SetContainers(Current3DWorld.GetListBiologicalObjectsOfType(Obj.comboBoxContainer.SelectedItem.ToString()));
if (Obj.InOrOut.radioButtonIn.Checked) Detection.SetContainersMode(0);
else Detection.SetContainersMode(1);
}
Obj.AssociatedBiologicalObjectList = Detection.HessianDetection((float)Obj.WindowForSpotDetection.numericUpDownSpotRadius.Value,
(float)Obj.WindowForSpotDetection.numericUpDownIntensityThreshold.Value,
(int)Obj.WindowForSpotDetection.numericUpDownSpotLocality.Value,
(double)Obj.WindowForSpotDetection.numericUpDownSphereDisplayRadius.Value);
Obj.richTextBoxInfo.AppendText(Obj.AssociatedBiologicalObjectList.Count + " objects detected.");
for (int i = 0; i < Obj.AssociatedBiologicalObjectList.Count; i++)
{
cBiologicalSpot TmpSpot = (cBiologicalSpot)Obj.AssociatedBiologicalObjectList[i];
TmpSpot.Name = Obj.textBoxName.Text + " " + i;
TmpSpot.SetType(Obj.textBoxName.Text);
// TmpSpot.ThumbnailnewImage = imageListForThumbnail.Images[Obj.AssociatedBiologicalObjectList[i].GetType() + ".jpg"];
// if (Obj.checkBoxIsDisplayName.Checked)
// TmpSpot.AddText(TmpSpot.Name, Current3DWorld, (double)Obj.ForText.numericUpDownArrowScale.Value, Obj.ForText.buttonChangeColorPositive.BackColor);
if (Obj.checkIsBoxPointingArrow.Checked)
{
cGeometric3DObject AssociatedArrow = TmpSpot.AttachPointingArrow((double)Obj.ForArrow.numericUpDownArrowScale.Value, Obj.ForArrow.buttonChangeColorPositive.BackColor);
Current3DWorld.AddGeometric3DObject(AssociatedArrow);
}
// TmpSpot.SetOpacity((double)Obj.ColorOpacity.numericUpDownValue.Value);
// // if the object it the Master then create a meta-object and put it inside
if (Obj.IsMasterObject())
{
cMetaBiologicalObject Cell = new cMetaBiologicalObject("Cell " + i, Current3DWorld.ListMetaObjectList[0], Obj.AssociatedBiologicalObjectList[i]);
// // Cell.AddObject(Obj.AssociatedBiologicalObjectList[i]);
Current3DWorld.ListMetaObjectList[0].Add(Cell);
}
// /*cMetaBiologicalObject Cell = */
// //Current3DWorld.ListMetaObjectList[0].AssociateWith(Current3DWorld.ListMetaObjectList[0].FindTheClosestVolumeFrom(TmpSpot.GetCentroid(), 20), TmpSpot);
}
// if (Obj.radioButtonColorSingle.Checked)
// Current3DWorld.AddBiological3DObjects(Obj.AssociatedBiologicalObjectList, Obj.buttonChangeColorPositive.BackColor, eColorMode.Regular);
// else if (Obj.radioButtonColorRandom.Checked)
// Current3DWorld.AddBiological3DObjects(Obj.AssociatedBiologicalObjectList, Obj.buttonChangeColorPositive.BackColor, eColorMode.Random);
// else if (Obj.radioButtonColorIndexed.Checked)
// Current3DWorld.AddBiological3DObjects(Obj.AssociatedBiologicalObjectList, Obj.buttonChangeColorPositive.BackColor, eColorMode.Indexed);
}
else if (Obj.radioButtonIsVolumeRendering.Checked)
{
Current3DWorld.AddVolume3D(new cVolumeRendering3D(this.AssociatedImage.SingleChannelImage[(int)Obj.numericUpDownChannel.Value],
new cPoint3D((float)Obj.WindowForPreProcessing.numericUpDownShiftX.Value, (float)Obj.WindowForPreProcessing.numericUpDownShiftY.Value, (float)Obj.WindowForPreProcessing.numericUpDownShiftZ.Value),
null, Current3DWorld));
// cVolume3D Volume = new cVolume3D(SeqToAnalyse, (int)Obj.numericUpDownChannel.Value, new cPoint3D((float)Obj.WindowForPreProcessing.numericUpDownShiftX.Value, (float)Obj.WindowForPreProcessing.numericUpDownShiftY.Value, (float)Obj.WindowForPreProcessing.numericUpDownShiftZ.Value));
// Current3DWorld.AddVolume3D(Volume, Color.Black, Obj.buttonChangeColorPositive.BackColor);
}
// Thread oThread = new Thread(new ThreadStart(Obj.DisplayDone));
}
#endregion
#region Objects Association
cMetaBiologicalObjectList MetaCellList = Current3DWorld.ListMetaObjectList[0];
// let's associate the objects
for (int k = 0; k < ListFormForControl.Count; k++)
{
FormForControl Obj = ListFormForControl.ElementAt(ListFormForControl.Count - k -1);
// that's a volume rendering ... no connection
if (Obj.radioButtonIsVolumeRendering.Checked) continue;
// the object is the master
if (Obj.IsMasterObject()) continue;
// this object has not connections ... is not associated to the master
if (Obj.comboBoxLinkToTheMaster.SelectedIndex == 0) continue;
cPoint3D ClosestPt = new cPoint3D(0, 0, 0);
foreach (cBiological3DVolume CurrentSubObj in Obj.AssociatedBiologicalObjectList)
{
cBiological3DVolume ObjectToIdentify = null;
switch (Obj.comboBoxLinkToTheMaster.SelectedIndex)
{
case 1: // association by distance to the master centroid
ObjectToIdentify = MetaCellList.FindTheClosestVolumeCentroidFrom(CurrentSubObj.GetCentroid(), (double)Obj.WindowDistanceToMaster.numericUpDownDistanceMaxToMaster.Value);
break;
case 2:
// //cBiological3DVolume CurrentVolume
ObjectToIdentify = MetaCellList.FindTheClosestVolumeFrom(CurrentSubObj, (double)Obj.WindowDistanceToMaster.numericUpDownDistanceMaxToMaster.Value, out ClosestPt);
break;
default:
break;
}
if (ObjectToIdentify == null) continue;
cMetaBiologicalObject Cell = MetaCellList.AssociateWith(ObjectToIdentify, CurrentSubObj);
// // -------------- draw information and links between the objects ---------------------
if (Obj.WindowDistanceToMaster.checkBoxDrawLinkToMasterCenter.Checked)
{
c3DLine CurrLine = new c3DLine(CurrentSubObj.GetCentroid(), ObjectToIdentify.GetCentroid());
Current3DWorld.AddGeometric3DObject(CurrLine);
//if (Obj.WindowDistanceToMaster.checkBoxDisplayBranchToCenterDistance.Checked)
// CurrLine.DisplayLenght(Current3DWorld, 0.4);
}
// // -------------- draw information and links between the objects ---------------------
if (Obj.WindowDistanceToMaster.checkBoxDrawLinkToMasterEdges.Checked)
{
c3DLine CurrLine1 = new c3DLine(CurrentSubObj.GetCentroid(), ClosestPt);
Current3DWorld.AddGeometric3DObject(CurrLine1);
//if(Obj.WindowDistanceToMaster.checkBoxDisplayBranchToEdgesDistance.Checked)
// CurrLine1.DisplayLenght(Current3DWorld, 0.4);
}
}
}
#endregion
#region Post Processings
for (int k = 0; k < ListFormForControl.Count; k++)
{
FormForControl Obj = ListFormForControl.ElementAt(ListFormForControl.Count - k - 1);
// the object is the master
// // if (!Obj.IsMasterObject()) continue;
if (!Obj.WindowForMaster.checkBoxDrawAssociatedDelaunay.Checked) continue;
foreach (cMetaBiologicalObject CurrentMeta in MetaCellList)
{
Current3DWorld.AddGeometric3DObject(CurrentMeta.GenerateDelaunay(2.0f,true));
}
}
if (PostProcessWindow.checkBoxRemoveUnAssociatedObjects.Checked)
{
int RemovedObjects = Current3DWorld.RemoveNonAssociatedObjects();
Console.WriteLine(RemovedObjects + " objects removed.");
}
// if (PostProcessWindow.checkBoxExportMetaObjectSignatures.Checked)
// {
// if (CurrentTable == null)
// {
// CurrentTable = new DataTable();
// if (CurrentExperiment == null)
// CurrentTable.Columns.Add(new DataColumn("Image Idx", typeof(int)));
// else
// {
// CurrentTable.Columns.Add(new DataColumn("Image Col.", typeof(int)));
// CurrentTable.Columns.Add(new DataColumn("Image Row", typeof(int)));
// }
// CurrentTable.Columns.Add(new DataColumn("Meta Object Name", typeof(string)));
// foreach (string DescName in MetaCellList[0].GetSignatureNames())
// CurrentTable.Columns.Add(new DataColumn(DescName, typeof(double)));
// CurrentTable.Columns.Add(new DataColumn("Class", typeof(double)));
// }
// foreach (cMetaBiologicalObject CurrentMeta in MetaCellList)
// {
// List<double> CurrentSignature = CurrentMeta.GetSignature();
// CurrentTable.Rows.Add();
// if (CurrentExperiment == null)
// {
// CurrentTable.Rows[CurrentTable.Rows.Count - 1][0] = IdxImageProcessed;
// CurrentTable.Rows[CurrentTable.Rows.Count - 1][1] = CurrentMeta.Name;
// for (int Idx = 0; Idx < CurrentSignature.Count; Idx++)
// CurrentTable.Rows[CurrentTable.Rows.Count - 1][Idx + 2] = CurrentSignature[Idx];
// }
// else
// {
// CurrentTable.Rows[CurrentTable.Rows.Count - 1][0] = CurrentExperiment.Column;
// CurrentTable.Rows[CurrentTable.Rows.Count - 1][1] = CurrentExperiment.Row;
// CurrentTable.Rows[CurrentTable.Rows.Count - 1][2] = CurrentMeta.Name;
// for (int Idx = 0; Idx < CurrentSignature.Count; Idx++)
// CurrentTable.Rows[CurrentTable.Rows.Count - 1][Idx + 3] = CurrentSignature[Idx];
// }
// // Current3DWorld.CopyMetaObjectSignatureToTable(CurrentMeta, 0);
// }
// if (DataGrid != null)
// {
// DataGrid.dataGridViewForResults.DataSource = CurrentTable;
// DataGrid.Update();
// IdxImageProcessed++;
// }
// }
#endregion
// //CurrentTable = new DataTable();
// if (CurrentExperiment == null)
// {
// if (PostProcessWindow.checkBoxDisplayBottomPlate.Checked) Current3DWorld.DisplayBottom(Color.FromArgb(255, 255, 255));
// Current3DWorld.SetBackgroundColor(PostProcessWindow.buttonChangeColorPositive.BackColor);
// Current3DWorld.Render();
// }
// // Current3DWorld.SetLinkToDataGridView(dataGridViewForClassif);
cViewer3D V3D = new cViewer3D();
V3D.SetInputData(Current3DWorld);
V3D.Run();
cDisplayToWindow DTW = new cDisplayToWindow();
DTW.SetInputData(V3D.GetOutPut());
DTW.Run();
DTW.Display();
}
private void ToolStripMenuItem_3DTest(object sender, EventArgs e)
{
Plugin3D NewPlug = new Plugin3D(this.AssociatedImage);
NewPlug.Show();
return;
c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(this.AssociatedImage.Width, this.AssociatedImage.Height, this.AssociatedImage.Depth),
new cPoint3D(1, 1, 1));
cVolumeDetection Detection = new cVolumeDetection(this.AssociatedImage, 2, false);
Detection.SetShift(new cPoint3D(0, 0, 0));
Detection.SetContainers(null);
List<cInteractive3DObject> AssociatedBiologicalObjectList = Detection.IntensityThreshold(150f,
10,
float.MaxValue);
for (int i = 0; i < AssociatedBiologicalObjectList.Count; i++)
{
cBiological3DVolume TmpVol = (cBiological3DVolume)AssociatedBiologicalObjectList[i];
// MyWorld.AddGeometric3DObject(TmpVol.AttachText("Object " + i, 5, Color.White));
// //if (Obj.checkIsBoxPointingArrow.Checked)
cGeometric3DObject AssociatedArrow = TmpVol.AttachPointingArrow(5f, Color.Tomato);
MyWorld.AddGeometric3DObject(AssociatedArrow);
AssociatedBiologicalObjectList[i].SetOpacity(/*(double)Obj.ColorOpacity.numericUpDownValue.Value*/0.5);
AssociatedBiologicalObjectList[i].Colour = Color.Red;
MyWorld.AddBiological3DObject(AssociatedBiologicalObjectList[i]);
}
MyWorld.AddVolume3D(new cVolumeRendering3D(this.AssociatedImage.SingleChannelImage[0], new cPoint3D(0, 0, 0), null, MyWorld));
MyWorld.BackGroundColor = Color.LightGray;// GhostWhite;
cViewer3D V3D = new cViewer3D();
V3D.SetInputData(MyWorld);
V3D.Run();
cDisplayToWindow DTW = new cDisplayToWindow();
DTW.SetInputData(V3D.GetOutPut());
DTW.Run();
DTW.Display();
}
