public void Create(cPoint3D MinPt, cPoint3D MaxPt, Color Colour)
{
Position = new cPoint3D(0, 0, 0);
this.Colour = Colour;
BoundingBox = vtkCubeSource.New();
BoundingBox.SetBounds(MinPt.X, MaxPt.X, MinPt.Y, MaxPt.Y, MinPt.Z, MaxPt.Z);
vtk_PolyDataMapper = vtkPolyDataMapper.New();
vtk_PolyDataMapper.SetInputConnection(BoundingBox.GetOutputPort());
CreateVTK3DObject(0);
}
private void CreateDelaunay(List<cPoint3D> ListPts, Color Colour, bool IsWire)
{
Position = new cPoint3D(0, 0, 0);
this.Colour = Colour;
vtkPoints ListCentroid = vtkPoints.New();
for (int i = 0; i < ListPts.Count; i++)
ListCentroid.InsertPoint(i, ListPts[i].X, ListPts[i].Y, ListPts[i].Z);
vtkPolyData profile = vtkPolyData.New();
profile.SetPoints(ListCentroid);
vtkDelaunay2D del = vtkDelaunay2D.New();
del.SetInput(profile);
del.SetTolerance(0.001);
vtk_PolyDataMapper = vtkPolyDataMapper.New();
vtk_PolyDataMapper.SetInputConnection(del.GetOutputPort());
CreateVTK3DObject(0);
if (IsWire) SetToWireFrame();
else SetToSurface();
}
public c3DSphere(cPoint3D Center, double Radius, Color Colour)
{
CreateSphere(Center, Radius, Colour, 16);
}
public PanelForParamCellPopulations(cPoint3D WorldDims, FormForSimuGenerator Parent)
{
InitializeComponent();
this.WorldDims = WorldDims;
this.Parent = Parent;
}
private void CreatePlane(cPoint3D Axis1, cPoint3D Axis2, cPoint3D Origin, Color Colour)
{
Position = new cPoint3D(Origin.X, Origin.Y, Origin.Z);
this.Colour = Colour;
Plane = vtkPlaneSource.New();
Plane.SetPoint1(Axis1.X, Axis1.Y, Axis1.Z);
Plane.SetPoint2(Axis2.X, Axis2.Y, Axis2.Z);
Plane.SetOrigin(0, 0, 0);
Plane.SetXResolution(1);
Plane.SetYResolution(1);
vtk_PolyDataMapper = vtkPolyDataMapper.New();
vtk_PolyDataMapper.SetInputConnection(Plane.GetOutputPort());
CreateVTK3DObject(0);
}
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 c3DWorld(Kitware.VTK.RenderWindowControl CurrentrenderWindowControl, Sequence Seq)
//{
// this.ren1 = CurrentrenderWindowControl.RenderWindow.GetRenderers().GetFirstRenderer();
// this.renWin = CurrentrenderWindowControl.RenderWindow;
// if (Seq == null)
// {
// Xres = Yres = Zres = 0;
// }
// else
// {
// Xres = Seq.XResolution;
// Yres = Seq.YResolution;
// Zres = Seq.ZResolution;
// }
// ListPolyDataMapper = new List<vtkPolyDataMapper>();
// ListObject = new List<cObject3D>();
// ListVolume = new List<cVolume3D>();
//}
/// <summary>
/// Create a 3D world
/// </summary>
/// <param name="CurrentrenderWindowControl">vtk Control</param>
/// <param name="Dimensions">in pixels</param>
/// <param name="Resolution">spatial resolutions</param>
public c3DWorld(cPoint3D Dimensions, cPoint3D Resolution, RenderWindowControl CurrentrenderWindowControl, int[] WinPos)
{
// int[] Pos = renWin.GetPosition();
//,
if (CurrentrenderWindowControl == null)
{
renWin = vtkRenderWindow.New();
renWin.LineSmoothingOn();
renWin.PointSmoothingOn();
renWin.SetWindowName("3D World");
renWin.BordersOn();
renWin.DoubleBufferOn();
renWin.SetSize(750, 500);
// if(WinPos!=null) renWin.SetPosition(WinPos[0], WinPos[1]);
// this.ren1 = CurrentrenderWindowControl.RenderWindow.GetRenderers().GetFirstRenderer();
//CurrentrenderWindowControl.RenderWindow;
}
//// Menu Strip Construction
//this.contextMenuStripActorPicker = new ContextMenuStrip();
//ToolStripMenuItem StripMenuItemDisplay = new ToolStripMenuItem("Display");
//contextMenuStripActorPicker.Items.Add(StripMenuItemDisplay);
this.ren1 = vtkRenderer.New();
//renWin = CurrentrenderWindowControl.RenderWindow;//vtkRenderWindow.New();
renWin.AddRenderer(ren1);
iren = new vtkRenderWindowInteractor();
iren.SetRenderWindow(renWin);
//iren.SetInteractorStyle(vtkInteractorStyleJoystickCamera.New());
iren.SetInteractorStyle(vtkInteractorStyleTrackballCamera.New());
// iren.SetInteractorStyle(vtkInteractorStyleTerrain.New());
// iren.LeftButtonPressEvt += new vtkObject.vtkObjectEventHandler(RenderWindow_LeftButtonPressEvt);
iren.KeyPressEvt += new vtkObject.vtkObjectEventHandler(RenderWindow_KeyPressEvt);
iren.RightButtonPressEvt += new vtkObject.vtkObjectEventHandler(RenderWindow_RightButtonPressEvt);
//Render();
//this.ren1 =
Xres = Resolution.X;
Yres = Resolution.Y;
Zres = Resolution.Z;
SizeX = (int)Dimensions.X;
SizeY = (int)Dimensions.Y;
SizeZ = (int)Dimensions.Z;
// double[] fp = ren1.GetActiveCamera().GetFocalPoint();
// double[] p = ren1.GetActiveCamera().GetPosition();
// ren1.GetActiveCamera().ParallelProjectionOn();
// double dist = Math.Sqrt((p[0] - fp[0]) * (p[0] - fp[0]) + (p[1] - fp[1]) * (p[1] - fp[1]) + (p[2] - fp[2]) * (p[2] - fp[2]));
// ren1.GetActiveCamera().SetPosition(fp[0], fp[1], fp[2] + dist*1000);
// ren1.GetActiveCamera().Zoom(2);
//ren1.Render();
// this.Render();
ListPolyDataMapper = new List<vtkPolyDataMapper>();
ListObject = new List<cObject3D>();
// Vtk_CameraViewOrientation = ren1.GetActiveCamera();
}
private void CreateSphere(cPoint3D Center, double Radius, Color Colour, int Precision)
{
Position = new cPoint3D(Center.X, Center.Y, Center.Z);
this.Radius = Radius;
this.Colour = Colour;
sphere = vtkSphereSource.New();
sphere.SetThetaResolution(Precision);
sphere.SetPhiResolution(Precision);
sphere.SetRadius(Radius);
vtk_PolyDataMapper = vtkPolyDataMapper.New();
vtk_PolyDataMapper.SetInputConnection(sphere.GetOutputPort());
CreateVTK3DObject(2);
}
private void buttonOK_Click(object sender, EventArgs e)
{
CellPopulation = new cListAgents(this.textBoxName.Text);
string CellType = comboBoxCellType.Text;
cCellCycle ClassicCellCycle = new cCellCycle(); // default cell cycle
cPoint3D InitialPos = null;
if (radioButtonPosWorldCenter.Checked)
InitialPos = new cPoint3D(this.WorldDim.X / 2, this.WorldDim.Y / 2, this.WorldDim.Z / 2);
for (int i = 0; i < (int)numericUpDownInitialCellNumber.Value; i++)
{
if (radioButtonPosManual.Checked)
{
InitialPos = new cPoint3D((double)numericUpDownManualX.Value,
(double)numericUpDownManualY.Value,
(double)numericUpDownManualZ.Value);
}
else if (radioButtonPosRandom.Checked)
{
InitialPos = new cPoint3D(RND.NextDouble() * this.WorldDim.X,
RND.NextDouble() * this.WorldDim.Y,
RND.NextDouble() * this.WorldDim.Z);
}
cCellType CurrentCellType = Parent.ListCellTypes.FindType(CellType);
if (CurrentCellType == null) continue;
cAgent NewCell = new cAgent(Parent.ListCellTypes.FindType(CellType), InitialPos, RND.NextDouble() /** ClassicCellCycle.ListProba.Count*/);
//new cCell(
// InitialPos,
// 2,
// RND.NextDouble() * ClassicCellCycle.ListProba.Count);
CellPopulation.Add(NewCell);
}
List<cClassForVariable> ListToReturn = new List<cClassForVariable>();
this.v_CellNumber.Cst_Value = (double)numericUpDownInitialCellNumber.Value;
ListToReturn.Add(this.v_CellNumber);
this.v_InitPosX.Cst_Value = (double)numericUpDownManualX.Value;
ListToReturn.Add(this.v_InitPosX);
this.v_InitPosY.Cst_Value = (double)numericUpDownManualY.Value;
ListToReturn.Add(this.v_InitPosY);
this.v_InitPosZ.Cst_Value = (double)numericUpDownManualZ.Value;
ListToReturn.Add(this.v_InitPosZ);
if (this.radioButtonVolumeFixed.Checked)
this.v_InitVol.IsConstant = true;
else
this.v_InitVol.IsConstant = false;
this.v_InitVol.Cst_Value = (double)numericUpDownInitialVolumeManual.Value;
ListToReturn.Add(this.v_InitVol);
ListToReturn.Add(this.v_InitPosType);
ListToReturn.Add(this.v_InitVolType);
this.ListVariables = new cListVariables(ListToReturn);
}
public void DisplayXYZ()
{
if (CompleteScreening == null) return;
int DescX = this.comboBoxDescriptorX.SelectedIndex;
int DescY = this.comboBoxDescriptorY.SelectedIndex;
int DescZ = this.comboBoxDescriptorZ.SelectedIndex;
if (DescX < 0) DescX = 0;
if (DescY < 0) DescY = 0;
if (DescZ < 0) DescZ = 0;
int[] Pos = new int[2];
Pos[0] = 0;
Pos[1] = 0;
if (CurrentWorld == null)
{
CurrentWorld = new c3DWorld(new cPoint3D(1000, 1000, 1000), new cPoint3D(ListScales[DescX], ListScales[DescY], ListScales[DescZ]), this.renderWindowControl1, Pos, CompleteScreening);
}
CurrentWorld.SetBackgroundColor(Color.Black);
CurrentWorld.ren1.RemoveAllViewProps();
// if (widget != null) widget.SetEnabled(0);
Series CurrentSeries = new Series("ScatterPoints");
double MinX = double.MaxValue;
double MinY = double.MaxValue;
double MinZ = double.MaxValue;
double MaxZ = double.MinValue;
double MaxX = double.MinValue;
double MaxY = double.MinValue;
double TempX, TempY, TempZ;
int Idx = 0;
cExtendPlateList ListPlate = new cExtendPlateList();
cMetaBiologicalObjectList ListMeta = new cMetaBiologicalObjectList("Test");
cBiologicalSpot CurrentSpot1 = new cBiologicalSpot(Color.White, new cPoint3D(0, 0, 0), 1, 4);
cMetaBiologicalObject Plate3D = new cMetaBiologicalObject("Data", ListMeta, CurrentSpot1);
if (!IsFullScreen)
ListPlate.Add(CompleteScreening.GetCurrentDisplayPlate());
else
ListPlate = CompleteScreening.ListPlatesActive;
vtkUnsignedCharArray colors = vtkUnsignedCharArray.New();
colors.SetName("colors");
colors.SetNumberOfComponents(3);
vtkPoints Allpoints = vtkPoints.New();
cExtendedList ListPtX = new cExtendedList();
cExtendedList ListPtY = new cExtendedList();
cExtendedList ListPtZ = new cExtendedList();
for (int i = 0; i < ListPlate.Count; i++)
{
cPlate CurrentPlate = ListPlate[i];
for (int IdxValue = 0; IdxValue < CompleteScreening.Columns; IdxValue++)
for (int IdxValue0 = 0; IdxValue0 < CompleteScreening.Rows; IdxValue0++)
{
cWell TmpWell = CurrentPlate.GetWell(IdxValue, IdxValue0, true);
if (TmpWell != null)
{
TempX = TmpWell.ListDescriptors[DescX].GetValue();
if (TempX < MinX) MinX = TempX;
if (TempX > MaxX) MaxX = TempX;
TempY = TmpWell.ListDescriptors[DescY].GetValue();
if (TempY < MinY) MinY = TempY;
if (TempY > MaxY) MaxY = TempY;
TempZ = TmpWell.ListDescriptors[DescZ].GetValue();
if (TempZ < MinZ) MinZ = TempZ;
if (TempZ > MaxZ) MaxZ = TempZ;
// cBiologicalSpot CurrentSpot = new cBiologicalSpot(TmpWell.GetColor(), new cPoint3D(TempX, TempY, TempZ), 1, 4);
List<char> Col = new List<char>();
Col.Add((char)(TmpWell.GetColor().R));
Col.Add((char)(TmpWell.GetColor().G));
Col.Add((char)(TmpWell.GetColor().B));
// IntPtr unmanagedPointer = Marshal.UnsafeAddrOfPinnedArrayElement(Col.ToArray(), 0);
//colors.InsertNextTupleValue(unmanagedPointer);
colors.InsertNextTuple3(Col[0], Col[1], Col[2]);
ListPtX.Add(TempX);
ListPtY.Add(TempY);
ListPtZ.Add(TempZ);
// CurrentSpot.Name = TmpWell.AssociatedPlate.Name + " - " + TmpWell.GetPosX() + "x" + TmpWell.GetPosY() + " :" + TmpWell.Name;
// CurrentSpot.ObjectType = TmpWell.AssociatedPlate.Name + " - " + TmpWell.GetPosX() + "x" + TmpWell.GetPosY() + " :" + TmpWell.Name;
// Plate3D.AddObject(CurrentSpot);
// CurrentWorld.AddBiological3DObject(CurrentSpot);
//CurrentSeries.Points.Add(TempX, TempY);
// if (IsFullScreen)
// CurrentSeries.Points[Idx].ToolTip = TmpWell.AssociatedPlate.Name + "\n" + TmpWell.GetPosX() + "x" + TmpWell.GetPosY() + " :" + TmpWell.Name;
// else
// CurrentSeries.Points[Idx].ToolTip = TmpWell.GetPosX() + "x" + TmpWell.GetPosY() + " :" + TmpWell.Name;
Idx++;
}
}
}
double MinValueX = ListPtX.Min();
double MaxValueX = ListPtX.Max();
cExtendedList NormX = ListPtX.Normalize(MinValueX, MaxValueX);
double MinValueY = ListPtY.Min();
double MaxValueY = ListPtY.Max();
cExtendedList NormY = ListPtY.Normalize(MinValueY, MaxValueY);
double MinValueZ = ListPtZ.Min();
double MaxValueZ = ListPtZ.Max();
cExtendedList NormZ = ListPtZ.Normalize(MinValueZ, MaxValueZ);
for (int IdxPt = 0; IdxPt < ListPtX.Count; IdxPt++)
Allpoints.InsertNextPoint(NormX[IdxPt], NormY[IdxPt], NormZ[IdxPt]);
vtkPolyData polydata = vtkPolyData.New();
polydata.SetPoints(Allpoints);
polydata.GetPointData().SetScalars(colors);
vtkSphereSource SphereSource = vtkSphereSource.New();
SphereSource.SetRadius(RadiusSphere);
vtkGlyph3D glyph3D = vtkGlyph3D.New();
glyph3D.SetColorModeToColorByScalar();
glyph3D.SetSourceConnection(SphereSource.GetOutputPort());
glyph3D.SetInput(polydata);
glyph3D.ScalingOff();
glyph3D.Update();
vtkPolyDataMapper mapper = vtkPolyDataMapper.New();
mapper.SetInputConnection(glyph3D.GetOutputPort());
vtkActor actor = vtkActor.New();
actor.SetMapper(mapper);
CurrentWorld.ren1.AddActor(actor);
if ((CompleteScreening.GetCurrentDisplayPlate().ListDRCRegions != null) && (CompleteScreening.GlobalInfo.OptionsWindow.checkBoxConnectDRCPts.Checked))
{
foreach (cDRC_Region TmpRegion in CompleteScreening.GetCurrentDisplayPlate().ListDRCRegions)
{
int cpt = 0;
cWell[][] ListWells = TmpRegion.GetListWells();
foreach (cWell[] item in ListWells)
{
for (int IdxWell = 0; IdxWell < item.Length - 1; IdxWell++)
{
//cWell TmpWell0 = CompleteScreening.GetCurrentDisplayPlate().GetWell(item[IdxWell], IdxValue0, true);
if ((item[IdxWell] != null) && (item[IdxWell + 1] != null) && (item[IdxWell].GetClass() >= -1))
{
double StartX = (item[IdxWell].ListDescriptors[DescX].GetValue() - MinValueX) / (MaxValueX - MinValueX);
double StartY = (item[IdxWell].ListDescriptors[DescY].GetValue() - MinValueY) / (MaxValueY - MinValueY);
double StartZ = (item[IdxWell].ListDescriptors[DescZ].GetValue() - MinValueZ) / (MaxValueZ - MinValueZ);
double EndX = (item[IdxWell + 1].ListDescriptors[DescX].GetValue() - MinValueX) / (MaxValueX - MinValueX);
double EndY = (item[IdxWell + 1].ListDescriptors[DescY].GetValue() - MinValueY) / (MaxValueY - MinValueY);
double EndZ = (item[IdxWell + 1].ListDescriptors[DescZ].GetValue() - MinValueZ) / (MaxValueZ - MinValueZ);
cPoint3D StartPt = new cPoint3D(StartX, StartY, StartZ);
cPoint3D EndPt = new cPoint3D(EndX, EndY, EndZ);
c3DLine NewLine = new c3DLine(StartPt, EndPt);
CurrentWorld.AddGeometric3DObject(NewLine);
}
}
}
/*List<cDRC> ListDRC = new List<cDRC>();
for (int i = 0; i < CompleteScreening.ListDescriptors.Count; i++)
{
if (CompleteScreening.ListDescriptors[i].IsActive())
{
cDRC CurrentDRC = new cDRC(TmpRegion, CompleteScreening.ListDescriptors[i]);
ListDRC.Add(CurrentDRC);
cpt++;
}
}
*/
//cDRCDisplay DRCDisplay = new cDRCDisplay(ListDRC, GlobalInfo);
//if (DRCDisplay.CurrentChart.Series.Count == 0) continue;
//DRCDisplay.CurrentChart.Location = new Point((DRCDisplay.CurrentChart.Width + 50) * 0, (DRCDisplay.CurrentChart.Height + 10 + DRCDisplay.CurrentRichTextBox.Height) * h++);
//DRCDisplay.CurrentRichTextBox.Location = new Point(DRCDisplay.CurrentChart.Location.X, DRCDisplay.CurrentChart.Location.Y + DRCDisplay.CurrentChart.Height + 5);
//WindowforDRCsDisplay.LChart.Add(DRCDisplay.CurrentChart);
//WindowforDRCsDisplay.LRichTextBox.Add(DRCDisplay.CurrentRichTextBox);
}
}
// vtkAxesActor axis = vtkAxesActor.New();
vtkAxisActor axisX = vtkAxisActor.New();
axisX.SetPoint1(0, 0, 0);
axisX.SetPoint2(1, 0, 0);
axisX.SetTickLocationToBoth();
axisX.SetDeltaMajor(0.1);
axisX.SetMajorTickSize(0);
axisX.MinorTicksVisibleOff();
//axisX.Maj
CurrentWorld.ren1.AddActor(axisX);
vtkAxisActor axisY = vtkAxisActor.New();
axisY.SetPoint1(0, 0, 0);
axisY.SetPoint2(0, 1, 0);
axisY.SetTickLocationToBoth();
axisY.SetDeltaMajor(0.1);
axisY.SetMajorTickSize(0.05);
axisY.MinorTicksVisibleOff();
CurrentWorld.ren1.AddActor(axisY);
vtkAxisActor axisZ = vtkAxisActor.New();
axisZ.SetPoint1(0, 0, 0);
axisZ.SetPoint2(0, 0, 1);
axisZ.SetTickLocationToBoth();
axisZ.SetDeltaMajor(0.1);
axisZ.SetMajorTickSize(0.05);
axisZ.MinorTicksVisibleOff();
CurrentWorld.ren1.AddActor(axisZ);
if (widget == null)
{
widget = vtkOrientationMarkerWidget.New();
axes = vtkAxesActor.New();
widget.SetOutlineColor(0.9300, 0.5700, 0.1300);
widget.SetInteractor(CurrentWorld.iren);
widget.SetViewport(0.0, 0.0, 0.4, 0.4);
widget.SetEnabled(0);
// widget.InteractiveOn();
if (this.comboBoxDescriptorX.SelectedItem == null)
axes.SetXAxisLabelText(this.comboBoxDescriptorX.Items[0].ToString());
else
axes.SetXAxisLabelText(this.comboBoxDescriptorX.SelectedItem.ToString());
if (this.comboBoxDescriptorY.SelectedItem == null)
axes.SetYAxisLabelText(this.comboBoxDescriptorY.Items[0].ToString());
else
axes.SetYAxisLabelText(this.comboBoxDescriptorY.SelectedItem.ToString());
if (this.comboBoxDescriptorZ.SelectedItem == null)
axes.SetZAxisLabelText(this.comboBoxDescriptorZ.Items[0].ToString());
else
axes.SetZAxisLabelText(this.comboBoxDescriptorZ.SelectedItem.ToString());
widget.SetOrientationMarker(axes);
}
else
{
if(this.comboBoxDescriptorX.SelectedItem!=null)
axes.SetXAxisLabelText(this.comboBoxDescriptorX.SelectedItem.ToString());
if (this.comboBoxDescriptorY.SelectedItem != null)
axes.SetYAxisLabelText(this.comboBoxDescriptorY.SelectedItem.ToString());
if (this.comboBoxDescriptorZ.SelectedItem != null)
axes.SetZAxisLabelText(this.comboBoxDescriptorZ.SelectedItem.ToString());
widget.SetOrientationMarker(axes);
}
//
//vtkCameraWidget Wid = vtkCameraWidget.New();
//Wid.SetInteractor(CurrentWorld.iren);
//Wid.SetEnabled(1);
// Wid.InteractiveOn();
//vtkDistanceWidget distanceWidget = vtkDistanceWidget.New();
//distanceWidget.SetInteractor(CurrentWorld.iren);
//distanceWidget.SetEnabled(1);
//distanceWidget.CreateDefaultRepresentation();
//((vtkDistanceRepresentation)distanceWidget.GetRepresentation()).SetLabelFormat("%-#6.3g mm");
/*static_cast<vtkDistanceRepresentation*>(distanceWidget->GetRepresentation())
->SetLabelFormat("%-#6.3g mm");
*/
// Plate3D.GenerateAndDisplayBoundingBox(1, Color.White, false, CurrentWorld);
//c3DText CaptionX = new c3DText(CurrentWorld, CompleteScreening.ListDescriptors[DescX].GetName(), new cPoint3D(MaxX, MinY, MinZ), Color.DarkRed, this.FontSize);
//c3DLine LineX = new c3DLine(new cPoint3D(MinX, MinY, MinZ), new cPoint3D(MaxX, MinY, MinZ), Color.DarkRed);
//CurrentWorld.AddGeometric3DObject(LineX);
//c3DText CaptionY = new c3DText(CurrentWorld, CompleteScreening.ListDescriptors[DescY].GetName(), new cPoint3D(MinX, MaxY, MinZ), Color.DarkGreen, this.FontSize);
//c3DLine LineY = new c3DLine(new cPoint3D(MinX, MinY, MinZ), new cPoint3D(MinX, MaxY, MinZ), Color.DarkGreen);
//CurrentWorld.AddGeometric3DObject(LineY);
//c3DText CaptionZ = new c3DText(CurrentWorld, CompleteScreening.ListDescriptors[DescZ].GetName(), new cPoint3D(MinX, MinY, MaxZ), Color.DarkBlue, this.FontSize);
//c3DLine LineZ = new c3DLine(new cPoint3D(MinX, MinY, MinZ), new cPoint3D(MinX, MinY, MaxZ), Color.DarkBlue);
//CurrentWorld.AddGeometric3DObject(LineZ);
CurrentWorld.SimpleRender();// Render();
}
private void Create3DDRC(cDRC DRCToDraw, cDRC_Region AssociatedRegion, Color Color, double Min, double Max)
{
if (DRCToDraw.ResultFit == null) return;
Position = new cPoint3D(AssociatedRegion.PosXMin + 0.5, AssociatedRegion.PosYMin + 0.2, 0);
this.Colour = Color;
vtkPoints points = vtkPoints.New();
vtkUnsignedCharArray colors = vtkUnsignedCharArray.New();
colors.SetName("Colors");
colors.SetNumberOfComponents(3);
colors.SetNumberOfTuples(AssociatedRegion.NumConcentrations);
for (int i = 0; i < AssociatedRegion.NumConcentrations; i++)
{
if (i >= DRCToDraw.ResultFit.Y_Estimated.Count) continue;
double PosZ = 8 - ((DRCToDraw.ResultFit.GetNormalizedY_Estimated()[i]) * 8);
points.InsertPoint(i, i, 0, PosZ);
colors.InsertTuple3(i / AssociatedRegion.NumConcentrations, i / AssociatedRegion.NumConcentrations, 255, i / AssociatedRegion.NumConcentrations);
}
Spline = vtkParametricSpline.New();
Spline.SetPoints(points);
Spline.ClosedOff();
vtkParametricFunctionSource SplineSource = vtkParametricFunctionSource.New();
SplineSource.SetParametricFunction(Spline);
// SplineSource.GetPolyDataInput(0).GetPointData().AddArray(colors);
vtkLinearExtrusionFilter extrude = vtkLinearExtrusionFilter.New();
extrude.SetInputConnection(SplineSource.GetOutputPort());
//extrude.GetPolyDataInput(0).GetPointData().AddArray(colors);
extrude.SetScaleFactor(AssociatedRegion.NumReplicate - 0.2);
//extrude.SetExtrusionTypeToNormalExtrusion();
extrude.SetExtrusionTypeToVectorExtrusion();
extrude.SetVector(0, 1, 0);
vtk_PolyDataMapper = vtkPolyDataMapper.New();
vtk_PolyDataMapper.SetInputConnection(extrude.GetOutputPort()/*SplineSource.GetOutputPort()*/);
vtk_PolyDataMapper.GetInput().GetPointData().AddArray(colors);
vtk_PolyDataMapper.ScalarVisibilityOn();
vtk_PolyDataMapper.SetScalarModeToUsePointFieldData();
vtk_PolyDataMapper.SelectColorArray("Colors");
CreateVTK3DObject(3);
}
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 double DistTo(cPoint3D DestPoint)
{
return Math.Sqrt((DestPoint.X - this.X) * (DestPoint.X - this.X) + (DestPoint.Y - this.Y) * (DestPoint.Y - this.Y) + (DestPoint.Z - this.Z) * (DestPoint.Z - this.Z));
}
public cPoint3D GetPosition()
{
cDescriptorType DescTypeForPosX = cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorByName(cGlobalInfo.OptionsWindow.comboBoxDescriptorForPosX.Text);
cDescriptorType DescTypeForPosY = cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorByName(cGlobalInfo.OptionsWindow.comboBoxDescriptorForPosY.Text);
if ((DescTypeForPosX == null) || (DescTypeForPosY == null))
{
this.Position = new cPoint3D(-1, -1, -1);
return this.Position;
}
return this.Position;
}
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;
}
public FormForInfoSingleCellPopInit_Simulator(cPoint3D WorldDim, cListVariables ListVariablesInput, FormForSimuGenerator Parent, cListAgents CellPopulation)
{
InitializeComponent();
if (CellPopulation == null)
{
this.comboBoxCellType.Text = "Regular";
this.ListVariables = ListVariablesInput;
this.textBoxName.Text = "Population_" + Parent.MyPanelForParamCellPopulations.listViewForCellPopulations.Items.Count;
}
else
{
this.comboBoxCellType.Text = CellPopulation[0].Type.Name;
this.textBoxName.Text = CellPopulation.Name;
ListVariables = CellPopulation.AssociatedVariables;
}
this.WorldDim = WorldDim;
this.Parent = Parent;
this.v_CellNumber = ListVariables.FindVariable("v_CellNumber");
this.v_InitPosX = ListVariables.FindVariable("v_InitPosX");
this.v_InitPosY = ListVariables.FindVariable("v_InitPosY");
this.v_InitPosZ = ListVariables.FindVariable("v_InitPosZ");
this.v_InitPosType = ListVariables.FindVariable("v_InitPosType");
this.v_InitVolType = ListVariables.FindVariable("v_InitVolType");
this.v_InitVol = ListVariables.FindVariable("v_InitVol");
if (v_InitVolType.Cst_Value == 0)
{
this.radioButtonVolumeRandom.Checked = false;
this.radioButtonVolumeFixed.Checked = true;
}
else if (v_InitVolType.Cst_Value == 10)
{
this.radioButtonVolumeRandom.Checked = true;
this.radioButtonVolumeFixed.Checked = false;
}
if (v_InitPosType.Cst_Value == 0)
{
this.radioButtonPosWorldCenter.Checked = true;
this.radioButtonPosRandom.Checked = false;
this.radioButtonPosManual.Checked = false;
}
else if (v_InitPosType.Cst_Value == 1)
{
this.radioButtonPosWorldCenter.Checked = false;
this.radioButtonPosRandom.Checked = true;
this.radioButtonPosManual.Checked = false;
}
else
{
this.radioButtonPosWorldCenter.Checked = false;
this.radioButtonPosRandom.Checked = false;
this.radioButtonPosManual.Checked = true;
}
this.numericUpDownInitialCellNumber.Value = (decimal)v_CellNumber.Cst_Value;
this.numericUpDownManualX.Value = (decimal)v_InitPosX.Cst_Value;
this.numericUpDownManualY.Value = (decimal)v_InitPosY.Cst_Value;
this.numericUpDownManualZ.Value = (decimal)v_InitPosZ.Cst_Value;
this.numericUpDownInitialVolumeManual.Value = (decimal)v_InitVol.Cst_Value;
if (v_InitVol.IsConstant)
{
this.radioButtonVolumeFixed.Checked = true;
this.radioButtonVolumeRandom.Checked = false;
}
else
{
this.radioButtonVolumeFixed.Checked = false;
this.radioButtonVolumeRandom.Checked = true;
}
this.comboBoxCellType.Items.Clear();
foreach (cCellType item in Parent.ListCellTypes)
this.comboBoxCellType.Items.Add(item.Name);
}
public c3DSphere(cPoint3D Center, double Radius, Color Colour, int Precision)
{
CreateSphere(Center, Radius, Colour, Precision);
}
// private cPoint3D Point2;
//private void CreateLine(cPoint3D Point1, cPoint3D Point2, Color Colour)
//{
// Position = new cPoint3D(Point1.X, Point1.Y, Point1.Z);
// Position = new cPoint3D(0, 0, 0);
// this.Colour = Colour;
// Line = vtkLineSource.New();
// this.Point1 = new cPoint3D(Point1.X, Point1.Y, Point1.Z);
// this.Point2 = new cPoint3D(Point2.X, Point2.Y, Point2.Z);
// Line.SetPoint1(Point1.X, Point1.Y, Point1.Z);
// Line.SetPoint2(Point2.X, Point2.Y, Point2.Z);
// vtk_PolyDataMapper = vtkPolyDataMapper.New();
// vtk_PolyDataMapper.SetInputConnection(Line.GetOutputPort());
// CreateVTK3DObject(0);
//}
public c3DText(c3DWorld CurrentWorld, string TextToDisplay, cPoint3D Position, Color Colour, double Scale)
{
// CreateLine(Point1, Point2, Colour);
vtkFollower TextActor = vtkFollower.New();
vtkPolyDataMapper TextMapper = vtkPolyDataMapper.New();
vtkVectorText TextVTK = vtkVectorText.New();
// double Dist = Point1.DistTo(Point2);
TextVTK.SetText(TextToDisplay);
TextMapper.SetInputConnection(TextVTK.GetOutputPort());
TextActor.SetMapper(TextMapper);
TextActor.SetPosition(Position.X, Position.Y, Position.Z);
TextActor.SetPickable(0);
TextActor.SetScale(Scale);
CurrentWorld.ren1.AddActor(TextActor);
TextActor.SetCamera(CurrentWorld.ren1.GetActiveCamera());
}
public c3DSphere(cPoint3D Center, double Radius)
{
CreateSphere(Center, Radius, Color.Red, 16);
}
private void Create(cDRC_Region AssociatedRegion, Color Color, double Regularization)
{
Position = new cPoint3D(AssociatedRegion.PosXMin + 1, AssociatedRegion.PosYMin + 0.7, 0);
List<cPoint3D> ListPtSigma = new List<cPoint3D> ( );
double GlobalMin = double.MaxValue;
double GlobalMax = double.MinValue;
for (int j = 0; j < AssociatedRegion.SizeY; j++)
for (int i = 0; i < AssociatedRegion.SizeX; i++)
{
cWell TmpWell = AssociatedRegion.GetListWells()[j][i];
if (TmpWell == null) continue;
double PosZ = TmpWell.ListDescriptors[TmpWell.AssociatedPlate.ParentScreening.ListDescriptors.CurrentSelectedDescriptor].GetValue();
if (PosZ >= GlobalMax) GlobalMax = PosZ;
if (PosZ <= GlobalMin) GlobalMin = PosZ;
ListPtSigma.Add(new cPoint3D(i/(double)AssociatedRegion.SizeX,PosZ,j/(double)AssociatedRegion.SizeY));
}
if (GlobalMax == GlobalMin) return;
double[,] ResultThinPlate = calc_tps(ListPtSigma, AssociatedRegion, Regularization);
if (ResultThinPlate == null)
{
// MessageBox.Show("Error in computing the associated thinplate !", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
// Position = new cPoint3D(0, 0, 0);
this.Colour = Color;
vtkPoints points = vtkPoints.New();
// vtkPoints points0 = vtkPoints.New();
//vtkUnsignedCharArray colors = vtkUnsignedCharArray.New();
//colors.SetName("Colors");
//colors.SetNumberOfComponents(3);
//colors.SetNumberOfTuples(AssociatedRegion.SizeX * AssociatedRegion.SizeY);
int Idx = 0;
for(int j=0;j<AssociatedRegion.SizeY;j++)
for (int i = 0; i < AssociatedRegion.SizeX; i++)
{
cWell TmpWell = AssociatedRegion.GetListWells()[j][i];
double PosZ = 8 - ( (ResultThinPlate[i,j]-GlobalMin)/(GlobalMax-GlobalMin))*8;
//points.InsertPoint(Idx,TmpWell.GetPosX(), TmpWell.GetPosY(), PosZ);
// points.InsertPoint(Idx, TmpWell.GetPosX(), TmpWell.GetPosY(), 0);
points.InsertPoint(Idx++, i, j, PosZ);
// colors.InsertTuple3(Idx++, 1, 1, 1);
}
vtkPolyData profile = vtkPolyData.New();
profile.SetPoints(points);
vtkDelaunay2D del = vtkDelaunay2D.New();
del.SetInput(profile);
del.SetTolerance(0.001);
vtkButterflySubdivisionFilter subdivisionFilter = vtkButterflySubdivisionFilter.New();
subdivisionFilter.SetInput(del.GetOutput());
subdivisionFilter.SetNumberOfSubdivisions(2);
subdivisionFilter.Update();
vtk_PolyDataMapper = vtkPolyDataMapper.New();
AlgoOutPut = subdivisionFilter.GetOutputPort();
vtk_PolyDataMapper.SetInputConnection(AlgoOutPut);
// vtk_PolyDataMapper.GetInput().GetPointData().AddArray(colors);
// vtk_PolyDataMapper.ScalarVisibilityOn();
// vtk_PolyDataMapper.SetScalarModeToUsePointFieldData();
// vtk_PolyDataMapper.SelectColorArray("Colors");
// vtkLinearExtrusionFilter extrude = vtkLinearExtrusionFilter.New();
// extrude.SetInput(cutter.GetOutput());
//extrude.SetScaleFactor(1);
//extrude.SetExtrusionTypeToNormalExtrusion();
//extrude.SetVector(1, 1, 1);
//vtkRotationalExtrusionFilter extrude = vtkRotationalExtrusionFilter.New();
//extrude.SetInput(cutter.GetOutput());
//extrude.SetResolution(60);
//extrude.Update();
//vtk_PolyDataMapper.SetInputConnection(tubeFilter.GetOutputPort());
CreateVTK3DObject(3);
SetColor(Color);
// SetOpacity(1);
SetToSurface();
}
public c3DLine(cPoint3D Point1, cPoint3D Point2, Color Colour)
{
CreateLine(Point1, Point2, Colour);
}
public cWorld(cPoint3D Dimensions, FormForSimuGenerator Parent)
{
this.Dimensions = new cPoint3D(Dimensions.X, Dimensions.Y, Dimensions.Z);
this.Parent = Parent;
}
/// <summary>
/// Compute the Thin Plate Spline of the image, return a 2D tab
/// </summary>
/// <param name="control_points">Control points </param>
/// <param name="input">Input image to get the dim xy</param>
public double[,] calc_tps(List<cPoint3D> control_points, cDRC_Region AssociatedRegion, double Regularization)
{
int p = control_points.Count;
if (p < 3) return null;
double[,] grid = new double[AssociatedRegion.SizeX, AssociatedRegion.SizeY];
Matrix mtx_l = new Matrix(p + 3, p + 3);
Matrix mtx_v = new Matrix(p + 3, 1);
Matrix mtx_orig_k = new Matrix(p, p);
double a = 0.0;
for (int i = 0; i < p; ++i)
{
for (int j = i + 1; j < p; ++j)
{
cPoint3D pt_i = new cPoint3D(control_points[i].X, control_points[i].Y, control_points[i].Z);
cPoint3D pt_j = new cPoint3D(control_points[j].X, control_points[j].Y, control_points[j].Z);
pt_i.Y = pt_j.Y = 0;
//double elen = Math.Sqrt((pt_i.X - pt_j.X) * (pt_i.X - pt_j.X) + (pt_i.Z - pt_j.Z) * (pt_i.Z - pt_j.Z));
double elen = pt_i.DistTo(pt_j);
mtx_l[i, j] = mtx_l[j, i] = mtx_orig_k[i, j] = mtx_orig_k[j, i] = tps_base_func(elen);
a += elen * 2; // same for upper & lower tri
}
}
a /= (double)(p * p);
//regularization = 0.3f;
//Fill the rest of L
for (int i = 0; i < p; ++i)
{
//diagonal: reqularization parameters (lambda * a^2)
mtx_l[i, i] = mtx_orig_k[i, i] = Regularization * (a * a);
// P (p x 3, upper right)
mtx_l[i, p + 0] = 1.0;
mtx_l[i, p + 1] = control_points[i].X;
mtx_l[i, p + 2] = control_points[i].Z;
// P transposed (3 x p, bottom left)
mtx_l[p + 0, i] = 1.0;
mtx_l[p + 1, i] = control_points[i].X;
mtx_l[p + 2, i] = control_points[i].Z;
}
// O (3 x 3, lower right)
for (int i = p; i < p + 3; ++i)
for (int j = p; j < p + 3; ++j)
mtx_l[i, j] = 0.0;
// Fill the right hand vector V
for (int i = 0; i < p; ++i)
mtx_v[i, 0] = control_points[i].Y;
mtx_v[p + 0, 0] = mtx_v[p + 1, 0] = mtx_v[p + 2, 0] = 0.0;
// Solve the linear system "inplace"
Matrix mtx_v_res = new Matrix(p + 3, 1);
LuDecomposition ty = new LuDecomposition(mtx_l);
mtx_v_res = ty.Solve(mtx_v);
if (mtx_v_res == null)
{
return null;
}
// Interpolate grid heights
for (int x = 0; x < AssociatedRegion.SizeX; ++x)
{
for (int z = 0; z < AssociatedRegion.SizeY; ++z)
{
//float x = 0f; float z = 0.5f;
double h = mtx_v_res[p + 0, 0] + mtx_v_res[p + 1, 0] * (float)x / (float)AssociatedRegion.SizeX + mtx_v_res[p + 2, 0] * (float)z / (float)AssociatedRegion.SizeY;
//double h = mtx_v[p + 0, 0] + mtx_v[p + 1, 0] * (float)x + mtx_v[p + 2, 0] * (float)z ;
cPoint3D pt_ia;
cPoint3D pt_cur = new cPoint3D((float)x / (float)AssociatedRegion.SizeX, 0, (float)z / (float)AssociatedRegion.SizeY);
//Vector3 pt_cur = new Vector3((float)x , 0, (float)z);
for (int i = 0; i < p; ++i)
{
pt_ia = control_points[i];
pt_ia.Y = 0;
h += mtx_v_res[i, 0] * tps_base_func(pt_ia.DistTo(pt_cur));
}
grid[x, z] = h;
}
}
// Calc bending energy
Matrix w = new Matrix(p, 1);
for (int i = 0; i < p; ++i)
w[i, 0] = mtx_v_res[i, 0];
Matrix be;
be = Matrix.Multiply(Matrix.Multiply(w.Transpose(), mtx_orig_k), w);
bending_energy = be[0, 0];
Console.WriteLine("be= " + be[0, 0]);
return grid;
}
public c3DLine(cPoint3D Point1, cPoint3D Point2)
{
CreateLine(Point1, Point2, Color.White);
}
private void CreateLine(cPoint3D Point1, cPoint3D Point2, Color Colour)
{
Position = new cPoint3D(Point1.X, Point1.Y, Point1.Z);
Position = new cPoint3D(0, 0, 0);
this.Colour = Colour;
Line = vtkLineSource.New();
this.Point1 = new cPoint3D(Point1.X, Point1.Y, Point1.Z);
this.Point2 = new cPoint3D(Point2.X, Point2.Y, Point2.Z);
Line.SetPoint1(Point1.X, Point1.Y, Point1.Z);
Line.SetPoint2(Point2.X, Point2.Y, Point2.Z);
vtk_PolyDataMapper = vtkPolyDataMapper.New();
vtk_PolyDataMapper.SetInputConnection(Line.GetOutputPort());
CreateVTK3DObject(0);
}
public c3DPlane(cPoint3D Point1, cPoint3D Point2, cPoint3D Origin, Color Colour)
{
CreatePlane(Point1, Point2, Origin, Colour);
}
public int KeepOnlyObjectsInsideTheOthers(List<cInteractive3DObject> ListContent, List<cInteractive3DObject> ListContainer)
{
int RemovedObjects = 0;
for (int IdxContent = 0; IdxContent < ListContent.Count; )
{
cInteractive3DObject CurrentContent = ListContent[IdxContent];
cPoint3D TestCentriolPt = new cPoint3D(CurrentContent.GetCentroid().X, CurrentContent.GetCentroid().Y, CurrentContent.GetCentroid().Z);
for (int IdxContainer = 0; IdxContainer < ListContainer.Count; IdxContainer++)
{
cBiological3DVolume CurrentVol = (cBiological3DVolume)ListContainer[IdxContainer];
// cPoint3D TestPt1 = new cPoint3D(CurrentVol.GetCentroid().X, CurrentVol.GetCentroid().Y, CurrentVol.GetCentroid().Z);
if (CurrentVol.IsPointInside(TestCentriolPt))
{
ListContent.Remove(CurrentContent);
RemovedObjects++;
}
}
}
return RemovedObjects;
}
public c3DPlane(cPoint3D Point1, cPoint3D Point2, cPoint3D Origin)
{
CreatePlane(Point1, Point2, Origin, Color.White);
}
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();
}
public void SetInputData(vtkExtractVOI Input, cPoint3D Pos)
{
this.VTKInput = Input;
this.Pos = Pos;
}
