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;
}
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;
}
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;
}
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();
}
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
}
