Example #1
0
        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);
        }
Example #2
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();
        }
Example #3
0
 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;
 }
Example #5
0
        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);
        }
Example #6
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;
        }
Example #7
0
        //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();
        }
Example #8
0
        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();
        }
Example #11
0
        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);
        }
Example #12
0
        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;
        }
Example #13
0
 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;
        }
Example #15
0
        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);
        }
Example #17
0
 public c3DSphere(cPoint3D Center, double Radius, Color Colour, int Precision)
 {
     CreateSphere(Center, Radius, Colour, Precision);
 }
Example #18
0
        // 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());
        }
Example #19
0
 public c3DSphere(cPoint3D Center, double Radius)
 {
     CreateSphere(Center, Radius, Color.Red, 16);
 }
Example #20
0
        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();
        }
Example #21
0
 public c3DLine(cPoint3D Point1, cPoint3D Point2, Color Colour)
 {
     CreateLine(Point1, Point2, Colour);
 }
Example #22
0
 public cWorld(cPoint3D Dimensions, FormForSimuGenerator Parent)
 {
     this.Dimensions = new cPoint3D(Dimensions.X, Dimensions.Y, Dimensions.Z);
     this.Parent = Parent;
 }
Example #23
0
        /// <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;
        }
Example #24
0
 public c3DLine(cPoint3D Point1, cPoint3D Point2)
 {
     CreateLine(Point1, Point2, Color.White);
 }
Example #25
0
        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);
        }
Example #26
0
 public c3DPlane(cPoint3D Point1, cPoint3D Point2, cPoint3D Origin, Color Colour)
 {
     CreatePlane(Point1, Point2, Origin, Colour);
 }
Example #27
0
        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;
        }
Example #28
0
 public c3DPlane(cPoint3D Point1, cPoint3D Point2, cPoint3D Origin)
 {
     CreatePlane(Point1, Point2, Origin, Color.White);
 }
Example #29
0
        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();
        }
Example #30
0
 public void SetInputData(vtkExtractVOI Input, cPoint3D Pos)
 {
     this.VTKInput = Input;
     this.Pos = Pos;
 }