Beispiel #1
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("Plate MetaObject");

            cImage I = this.Input.GetClassColorImage();

              //  cDisplaySingleImage DSI = new cDisplaySingleImage();
              //  DSI.SetInputData(I);
              //  DSI.Run();

            c3DTexturedPlan PlateTexture = new c3DTexturedPlan(new cPoint3D(0, 0, 0), I);

            //c3DTexturedPlan PlateTexture = new c3DTexturedPlan(new cPoint3D(0,0,0),this.Input.GetColorImage());
            PlateTexture.SetName(Input.GetShortInfo());
            PlateTexture.Tag = this.Input;
             //   List<byte[][]> TmpLut = new List<byte[][]>();
              //  TmpLut.Add(cGlobalInfo.CurrentPlateLUT);
              //  PlateTexture.LUT = TmpLut ;
            PlateTexture.Run();

            ListObjects.AddObject(PlateTexture);
            ListObjects[0].Tag = ListObjects.Tag = this.Input;

            ListObjects.AddObject(new c3DText(this.Input.GetName(), new cPoint3D(-12-1.2, -8-1.2, 0.2), Color.Black, 70));

            return base.FeedBackMessage;
        }
Beispiel #2
0
 public Form3DTreeView(c3DNewWorld AssociatedWorld)
 {
     InitializeComponent();
     this.AssociatedWorld = AssociatedWorld;
     this.treeViewFor3DObjects.NodeMouseClick += new TreeNodeMouseClickEventHandler(treeViewFor3DObjects_NodeMouseClick);
     this.treeViewFor3DObjects.MouseDown += new MouseEventHandler(treeViewFor3DObjects_MouseDown);
     RefreshTree();
 }
        public cFeedBackMessage Run(c3DNewWorld _3DWorld)
        {
            if (this.Input == null)
            {
                FeedBackMessage.IsSucceed = false;
                FeedBackMessage.Message = "No input data table defined.";
                return FeedBackMessage;
            }

            ListObjects = new cListGeometric3DObject("Screening MetaObject");

            int IdxPlate = 0;
            int Pos = 0;
            foreach (cPlate item in this.Input.ListPlatesActive)
            {
                c3DObject_Plate2D P2D = new c3DObject_Plate2D();
                P2D.SetInputData(item);
                P2D.Run(_3DWorld);
                foreach (var itemObj in P2D.GetOutPut())
                {
                    cPoint3D CurrentObjPos = itemObj.GetPosition() + new cPoint3D(Pos, 0, 0);
                    itemObj.SetPosition(CurrentObjPos);
                }

                //P2D.GetOutPut()[0].Tag = item;

                Pos += this.Input.Columns + 10;

                //c3DTexturedPlan PlateTexture = new c3DTexturedPlan(new cPoint3D(0,0,0),this.Input.GetColorImage());
                //PlateTexture.SetName(Input.());
                //PlateTexture.Tag = this.Input;
                //List<byte[][]> TmpLut = new List<byte[][]>();
                //TmpLut.Add(cGlobalInfo.CurrentPlateLUT);
                //PlateTexture.LUT = TmpLut ;
                //PlateTexture.Run();

                foreach (var itemObj in P2D.GetOutPut())
                {
                    ListObjects.AddObject(itemObj);
                }

                IdxPlate++;
            }

            ListObjects.Tag = this.Input;

            return base.FeedBackMessage;
        }
        public cFeedBackMessage Run(c3DNewWorld _3DWorld)
        {
            if (base.Start() == false)
            {
                base.FeedBackMessage.IsSucceed = false;
                return base.FeedBackMessage;
            }

            //if (this.Input == null)
            //{
            //    FeedBackMessage.IsSucceed = false;
            //    FeedBackMessage.Message = "No input data table defined.";
            //    return FeedBackMessage;
            //}

            #region Properties Management
            object _firstValue = base.ListProperties.FindByName("Normalized ?");
            bool IsNormalized = false;
            if (_firstValue == null)
            {
                base.GenerateError("-Normalized ?- not found !");
                return base.FeedBackMessage;
            }
            try
            {
                cProperty TmpProp = (cProperty)_firstValue;
                IsNormalized = (bool)TmpProp.GetValue();
            }
            catch (Exception)
            {
                base.GenerateError("-Normalized ?- cast didn't work");
                return base.FeedBackMessage;
            }

            _firstValue = base.ListProperties.FindByName("Draw Axis ?");
            bool IsdrawAxis = true;
            if (_firstValue == null)
            {
                base.GenerateError("-Draw Axis ?- not found !");
                return base.FeedBackMessage;
            }
            try
            {
                cProperty TmpProp = (cProperty)_firstValue;
                IsdrawAxis = (bool)TmpProp.GetValue();
            }
            catch (Exception)
            {
                base.GenerateError("-Draw Axis ?- cast didn't work");
                return base.FeedBackMessage;
            }

            _firstValue = base.ListProperties.FindByName("Link Points ?");
            bool IsLinked = false;
            if (_firstValue == null)
            {
                base.GenerateError("-Link Points ?- not found !");
                return base.FeedBackMessage;
            }
            try
            {
                cProperty TmpProp = (cProperty)_firstValue;
                IsLinked = (bool)TmpProp.GetValue();
            }
            catch (Exception)
            {
                base.GenerateError("-Link Points ?- cast didn't work");
                return base.FeedBackMessage;
               }
            #endregion

            cExtendedList ListLenghtsMax = new cExtendedList();

            ListObjects = new cListGeometric3DObject("Scatter Plot MetaObject");

            double MinX = this.Input.Min(0);
            double MaxX = this.Input.Max(0);
            double DeltaX = MaxX - MinX;
            ListLenghtsMax.Add(DeltaX);
            if (DeltaX == 0) DeltaX = 1;

            double MinY = this.Input.Min(1);
            double MaxY = this.Input.Max(1);
            double DeltaY = MaxY - MinY;
            ListLenghtsMax.Add(DeltaY);
            if (DeltaY == 0) DeltaY = 1;

            double MinZ = this.Input.Min(2);
            double MaxZ = this.Input.Max(2);
            double DeltaZ = MaxZ - MinZ;
            ListLenghtsMax.Add(DeltaZ);
            if (DeltaZ == 0) DeltaZ = 1;

            double MinRad = 0;
            double MaxRad = 0;
            double DeltaRad = 1;

            double MaxLenght = ListLenghtsMax.Min();
            if (MaxLenght <= 0) MaxLenght = 1;

            for (int CurrentSerie = 0; CurrentSerie < this.Input.Count; CurrentSerie++)
            {
                cExtendedTable CurrentTable = this.Input[CurrentSerie];
                if ((IndexColumnForSphereRadius > 0) && (IndexColumnForSphereRadius < CurrentTable.Count))
                {
                    MinRad = CurrentTable[IndexColumnForSphereRadius].Min();
                    MaxRad = CurrentTable[IndexColumnForSphereRadius].Max();

                    if (MaxRad != MinRad)
                        DeltaRad = MaxRad - MinRad;
                }

                if (CurrentTable.Count == 0) continue;

                cListGeometric3DObject TmpListObjects = new cListGeometric3DObject("Scatter MetaObject");
                TmpListObjects.Tag = CurrentTable.Tag;
                cPoint3D Pt = null;
                for (int IdxPt = 0; IdxPt < CurrentTable[0].Count; IdxPt++)
                {
                    if(IsNormalized)
                    Pt = new cPoint3D((CurrentTable[0][IdxPt] - MinX) / DeltaX, (CurrentTable[1][IdxPt] - MinY) / DeltaY, (CurrentTable[2][IdxPt] - MinZ) / DeltaZ);
                    else
                    Pt = new cPoint3D(CurrentTable[0][IdxPt], CurrentTable[1][IdxPt], CurrentTable[2][IdxPt]);

                    double Rad = this.Radius;
                    if ((IndexColumnForSphereRadius > 0) && (IndexColumnForSphereRadius < CurrentTable.Count))
                    {
                        Rad = this.Radius * ((CurrentTable[IndexColumnForSphereRadius][IdxPt] - MinRad)) / DeltaRad;
                        Rad /= 200;
                    }

                    if(IndexColumnForSphereRadius>-1)
                    Rad = CurrentTable[IndexColumnForSphereRadius][IdxPt];

                    if (IsNormalized) Rad /= 300.0;
                    else
                    {
                        Rad = MaxLenght / 100.0;
                    }

                    c3DSphere Sphere = new c3DSphere(Pt, Rad);
                    //c3DPoint Sphere = new c3DPoint(Pt);
                    if ((CurrentTable.ListRowNames != null) && (CurrentTable.ListRowNames.Count > IdxPt))
                    {
                        if (CurrentTable.ListRowNames[IdxPt] != null) Sphere.SetName(CurrentTable.ListRowNames[IdxPt]);
                        else
                            Sphere.SetName("Sphere " + IdxPt);
                    }
                    else
                    {
                        Sphere.SetName("Sphere " + IdxPt);
                    }

                    if ((CurrentTable.ListTags != null) && (CurrentTable.ListTags[IdxPt] != null) && (CurrentTable.ListTags[IdxPt].GetType() == typeof(cWell)))
                    {
                        if (CurrentTable.ListTags[IdxPt].GetType() == typeof(cWell))
                        {
                            Sphere.Colour = ((cWell)(CurrentTable.ListTags[IdxPt])).GetClassType().ColourForDisplay;
                            Sphere.Tag = CurrentTable.ListTags[IdxPt];
                        }
                    }
                    else //if (this.GlobalInfo != null)
                    {
                        Sphere.Colour = cGlobalInfo.ListCellularPhenotypes[CurrentSerie % cGlobalInfo.ListCellularPhenotypes.Count].ColourForDisplay;
                    }

                    TmpListObjects.AddObject(Sphere);

                    if ((ValueToBeDisplayed > 0) && (ValueToBeDisplayed < CurrentTable.Count))
                    {
                        if (_3DWorld != null)
                            TmpListObjects.Add(new c3DText(_3DWorld, CurrentTable[ValueToBeDisplayed][IdxPt].ToString("N3"), new cPoint3D(Pt.X + 0.02, Pt.Y + 0.02, Pt.Z + 0.02), Color.White, 0.01));
                    }
                }

                ListObjects.AddRange(TmpListObjects);

                #region Draw Links
                if (IsLinked)
                {
                    cListGeometric3DObject ListLinks = new cListGeometric3DObject( "Links MetaObject");

                    for (int IdxPt = 1; IdxPt < CurrentTable[0].Count; IdxPt++)
                    {
                        cPoint3D Pt1 = null;
                        cPoint3D Pt0 = null;

                        if (IsNormalized)
                        {
                            Pt1 = new cPoint3D((CurrentTable[0][IdxPt] - MinX) / DeltaX, (CurrentTable[1][IdxPt] - MinY) / DeltaY, (CurrentTable[2][IdxPt] - MinZ) / DeltaZ);
                            Pt0 = new cPoint3D((CurrentTable[0][IdxPt - 1] - MinX) / DeltaX, (CurrentTable[1][IdxPt - 1] - MinY) / DeltaY, (CurrentTable[2][IdxPt - 1] - MinZ) / DeltaZ);
                        }
                        else
                        {
                            Pt1 = new cPoint3D(CurrentTable[0][IdxPt], CurrentTable[1][IdxPt] , CurrentTable[2][IdxPt] );
                            Pt0 = new cPoint3D(CurrentTable[0][IdxPt - 1] , CurrentTable[1][IdxPt - 1] , CurrentTable[2][IdxPt - 1] );
                        }
                       // new cPoint3D((CurrentTable[0][IdxPt] - MinX) / DeltaX, (CurrentTable[1][IdxPt] - MinY) / DeltaY, (CurrentTable[2][IdxPt] - MinZ) / DeltaZ);
                        //cPoint3D Pt0 = new cPoint3D((CurrentTable[0][IdxPt - 1] - MinX) / DeltaX, (CurrentTable[1][IdxPt - 1] - MinY) / DeltaY, (CurrentTable[2][IdxPt - 1] - MinZ) / DeltaZ);

                        c3DLine Line = new c3DLine(Pt0, Pt1);
                        Line.SetName("Link ["+(IdxPt-1)+";"+IdxPt+"]");
                        ListLinks.AddObject(Line);
                    }

                    ListObjects.AddRange(ListLinks);
                }
                #endregion

            }

            #region Draw Axis
            if (IsdrawAxis && (this.Input[0].Count > 2))
            {
                c3DObject_Axis Axis = new c3DObject_Axis();
                cExtendedTable T = new cExtendedTable();
                T.Add(new cExtendedList(Input[0][0].Name));
                if (IsNormalized)
                {
                    T[0].Tag = Input[0][0].Tag;
                    T[0].Add(0);
                    T[0].Add(1);
                    T.Add(new cExtendedList(Input[0][1].Name));
                    T[1].Tag = Input[0][1].Tag;
                    T[1].Add(0);
                    T[1].Add(1);
                    T.Add(new cExtendedList(Input[0][2].Name));
                    T[2].Tag = Input[0][2].Tag;
                    T[2].Add(0);
                    T[2].Add(1);
                }
                else
                {
                    T[0].Tag = Input[0][0].Tag;
                    T[0].Add(MinX);
                    T[0].Add(MaxX);
                    T.Add(new cExtendedList(Input[0][1].Name));
                    T[1].Tag = Input[0][1].Tag;
                    T[1].Add(MinY);
                    T[1].Add(MaxY);
                    T.Add(new cExtendedList(Input[0][2].Name));
                    T[2].Tag = Input[0][2].Tag;
                    T[2].Add(MinZ);
                    T[2].Add(MaxZ);
                }

                Axis.SetInputData(T);
                Axis.Run(_3DWorld);

                ListObjects.AddRange(Axis.GetOutPut());
            }
            #endregion

            // _3DWorld.AddGeometric3DObjects(this.ListObjects);

            return base.FeedBackMessage;
        }
Beispiel #5
0
        private void ToolStripMenuItem_Display3DTexture(object sender, EventArgs e)
        {
            cViewer3D V3D = new cViewer3D();
            c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));

            cListGeometric3DObject GlobalList = new cListGeometric3DObject("2D Texture Metaobject");

            c3DTexturedPlan _3DPlan = new c3DTexturedPlan(new cPoint3D(0, 0, 0), this.AssociatedImage);

            //   c3DElevationMap _3DMap = new c3DElevationMap(new cPoint3D(0, 0, 0), this.Input, this.LUT);

            _3DPlan.SetName("2D Texture");
            _3DPlan.Run();
            GlobalList.Add(_3DPlan);

            foreach (var item in GlobalList)
                MyWorld.AddGeometric3DObject(item);

            //  MyWorld.AddLight(Color.White);

            V3D.SetInputData(MyWorld);
            V3D.Run();

            cDisplayToWindow DTW = new cDisplayToWindow();
            DTW.SetInputData(V3D.GetOutPut());
            DTW.Title = "2D texture (" + this.AssociatedImage.Name + ")";
            DTW.Run();
            DTW.Display();
        }
Beispiel #6
0
        void baseInit(c3DNewWorld AssociatedWorld)
        {
            this.WindowVolumeRenderingOption = new FormForVolumeRenderingOption(this);
            //this.WindowVolumeRenderingOption.Visible = false;
            this.WindowVolumeRenderingOption.Show();
            this.WindowVolumeRenderingOption.Visible = false;

            this.AssociatedWorld = AssociatedWorld;
        }
Beispiel #7
0
        private void basic3DToolStripMenuItem_Click(object sender, EventArgs e)
        {
            cViewer3D V3D = new cViewer3D();
            c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));

            c3DTexturedPlan Plan = new c3DTexturedPlan(new cPoint3D(0, 0, 0), new cImage(256, 256, 1, 1));
            Plan.Run();
            MyWorld.AddGeometric3DObject(Plan);

            V3D.SetInputData(MyWorld);
            V3D.Run();

            cDisplayToWindow DTW = new cDisplayToWindow();
            DTW.SetInputData(V3D.GetOutPut());
            DTW.Run();
            DTW.Display();
        }
Beispiel #8
0
        private void dDisplayToolStripMenuItem_Click(object sender, EventArgs e)
        {
            cViewer3D V3D = new cViewer3D();
            c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));

            MyWorld.BackGroundColor = cGlobalInfo.OptionsWindow.FFAllOptions.panelFor3DBackColor.BackColor;

            V3D.SetInputData(MyWorld);
            V3D.Run();


            cDesignerSinglePanel CD = new cDesignerSinglePanel();
            CD.SetInputData(V3D.GetOutPut());
            if (CD.Run().IsSucceed == false) return;

            cDisplayToWindow CDW = new cDisplayToWindow();
            CDW.SetInputData(CD.GetOutPut());
            CDW.Title = "3D world";
            if (CDW.Run().IsSucceed == false) return;
            CDW.Display();
        }
Beispiel #9
0
 public void SetInputData(c3DNewWorld Input)
 {
     this.Input = Input;
 }
Beispiel #10
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;
        }
Beispiel #11
0
        private void ToolStripMenuItem_Display3DScatterGraph(object sender, EventArgs e)
        {
            cExtendedTable CET = new cExtendedTable();

            foreach (DataGridViewColumn item in GridView.SelectedColumns)
            {
                CET.Add(Input[item.Index]);
            }

            if (this.Input.ListTags != null)
            {
                CET.ListTags = new List<object>();
                foreach (var item in this.Input.ListTags)
                {
                    CET.ListTags.Add(item);
                }
            }

            cListExtendedTable LET = new cListExtendedTable();
            LET.Add(CET);

            //List<cListWells> ListWells = new List<cListWells>();
            //ListWells.Add(cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().ListActiveWells);

            cViewer3D V3D = new cViewer3D();
            c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));

            c3DObjectScatterPoints _3DScatterPt = new c3DObjectScatterPoints();
            _3DScatterPt.ListProperties.FindByName("Draw Axis ?").SetNewValue((bool)true);
            _3DScatterPt.ListProperties.FindByName("Draw Axis ?").IsGUIforValue = true;
            _3DScatterPt.ListProperties.FindByName("Normalized ?").SetNewValue((bool)true);
            _3DScatterPt.ListProperties.FindByName("Normalized ?").IsGUIforValue = true;
            _3DScatterPt.ListProperties.FindByName("Link Points ?").SetNewValue((bool)false);
            _3DScatterPt.ListProperties.FindByName("Link Points ?").IsGUIforValue = true;

            //_3DScatterPt.GlobalInfo = cGlobalInfo;
            _3DScatterPt.SetInputData(LET);
            if (_3DScatterPt.Run(MyWorld).IsSucceed == false) return;

            cListGeometric3DObject GlobalList = _3DScatterPt.GetOutPut();

            foreach (var item in GlobalList)
            {
                MyWorld.AddGeometric3DObject(item);
            }

            V3D.SetInputData(MyWorld);
            V3D.Run();

            cDisplayToWindow DTW = new cDisplayToWindow();
            DTW.SetInputData(V3D.GetOutPut());
            DTW.Title = "3D Scatter Graph ("+ this.Input.Name +")";
            DTW.Run();
            DTW.Display();
        }
        public cFeedBackMessage Run(c3DNewWorld _3DWorld)
        {
            if (base.Start() == false)
            {
                base.FeedBackMessage.IsSucceed = false;
                return base.FeedBackMessage;
            }

            #region Properties Management
            object _firstValue = base.ListProperties.FindByName("Thresold");
            double Thresold = 0.5;
            if (_firstValue == null)
            {
                base.GenerateError("-Thresold- not found !");
                return base.FeedBackMessage;
            }
            try
            {
                cProperty TmpProp = (cProperty)_firstValue;
                Thresold = (double)TmpProp.GetValue();
            }
            catch (Exception)
            {
                base.GenerateError("-Thresold- cast didn't work");
                return base.FeedBackMessage;
            }

            _firstValue = base.ListProperties.FindByName("Split objects ?");
            bool IsSplit = false;
            if (_firstValue == null)
            {
                base.GenerateError("-Split objects ?- not found !");
                return base.FeedBackMessage;
            }
            try
            {
                cProperty TmpProp = (cProperty)_firstValue;
                IsSplit = (bool)TmpProp.GetValue();
            }
            catch (Exception)
            {
                base.GenerateError("-Split objects ?- cast didn't work");
                return base.FeedBackMessage;
            }
            #endregion

            ListObjects = new cListGeometric3DObject("");

            if (IsSplit == false)
            {
                c3DMeshObject MyMesh = null;

                if (this.VTKInput == null)
                {
                    MyMesh = new c3DMeshObject(this.Input, Thresold);
                }
                else
                {
                    MyMesh = new c3DMeshObject(this.VTKInput, (int)Thresold);

                }
                MyMesh.Create(Color.Aqua, this.Pos );
                ListObjects.Name = MyMesh.GetName() + " metaobject";
                ListObjects.Add(MyMesh);

            }
            else
            {
                // ok that's a little bit more complicated now
                // first we need to binarize the image
                cImageSegmentationThreshold IST = new cImageSegmentationThreshold();
                IST.ListProperties.FindByName("Threshold").SetNewValue(Thresold);
                cImage SourceImage = new cImage(this.Input, false);
                IST.SetInputData(SourceImage);
                IST.Run();

                // now perform image labeling
                cImage BinImage = IST.GetOutPut();
                cImage LabeledImage = new cImage(BinImage, false);
                ConnectedComponentSet CCS = new ConnectedComponentSet(BinImage,LabeledImage,SourceImage,  0, eConnectivity.THREED_6, 0, float.MaxValue);

                Random RD = new Random();

                int IdxObj = 1;
                // loop over each object
                int NumObj = CCS.Count;

                ListObjects.Name = "T_" + Thresold + " [" + SourceImage.Name + " Metaobject";

                for(int i = 0;i<NumObj;i++)
                {
                    ConnectedVoxels item = CCS[i];

                 //   if (item.Volume <= 1) continue;

                    List<cPoint3D> ExtremePts = item.GetExtremaPoints();
                    // crop the labeled image
                    cImage TmpIm = LabeledImage.Crop(ExtremePts[0], ExtremePts[1]);

                    // we have to clean the cropped image to prevent any overlapping object to be segmented
                    for (int Pix = 0; Pix < TmpIm.ImageSize; Pix++)
                    {
                        if ((TmpIm.SingleChannelImage[0].Data[Pix] > 0) && (TmpIm.SingleChannelImage[0].Data[Pix] != IdxObj)) TmpIm.SingleChannelImage[0].Data[Pix] = 0;
                    }

                    // update the position of the object
                    cPoint3D NewPos = ExtremePts[0]*SourceImage.Resolution;

                    c3DMeshObject MyMesh = new c3DMeshObject(TmpIm.SingleChannelImage[0], 0.5);
                    MyMesh.Create(Color.FromArgb(RD.Next(255), RD.Next(255), RD.Next(255)), NewPos);

                    MyMesh.SetName(MyMesh.GetName() + "_" + IdxObj);
                    MyMesh.AssociatedConnectedComponent = item;
                    ListObjects.AddObject(MyMesh);

                    IdxObj++;
                }

            }
            return base.FeedBackMessage;
        }
Beispiel #13
0
        public void Refresh3DScreenView()
        {
            cViewer3D V3D = new cViewer3D();
            c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));
            V3D.SetInputData(MyWorld);

            c3DObject_Screening2D Screening2D = new c3DObject_Screening2D();
            Screening2D.SetInputData(cGlobalInfo.CurrentScreening);
            Screening2D.Run(MyWorld);
            MyWorld.AddGeometric3DObjects(Screening2D.GetOutPut());

               // c3DObject_Plate2D Plate2D = new c3DObject_Plate2D();
               // Plate2D.SetInputData(this);
               // Plate2D.Run(MyWorld);
               // MyWorld.AddGeometric3DObjects(Plate2D.GetOutPut());

               // MyWorld.BackGroundColor = Color.White;

            V3D.Run();

            cExtendedControl EXT = V3D.GetOutPut();
            cGlobalInfo.WindowHCSAnalyzer.tabPage3DPlatesView.Controls.Clear();

            EXT.Width = cGlobalInfo.WindowHCSAnalyzer.tabPage3DPlatesView.Width;
            EXT.Height = cGlobalInfo.WindowHCSAnalyzer.tabPage3DPlatesView.Height;

            // EXT.Controls[0].Width = cGlobalInfo.WindowHCSAnalyzer.tabPage3DPlatesView.Width;
            // EXT.Controls[0].Height = cGlobalInfo.WindowHCSAnalyzer.tabPage3DPlatesView.Height;

            cGlobalInfo.WindowHCSAnalyzer.tabPage3DPlatesView.Controls.Add(EXT);

            //cDesignerSinglePanel CD = new cDesignerSinglePanel();
            //CD.SetInputData(V3D.GetOutPut());
            //if (CD.Run().IsSucceed == false) return;

            //cDisplayToWindow CDW = new cDisplayToWindow();
            //CDW.SetInputData(CD.GetOutPut());
            //CDW.Title = "3D world";
            //if (CDW.Run().IsSucceed == false) return;
            //CDW.Display();
        }
        private void GenerateGraph()
        {
            V3D = new cViewer3D();
            MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));

            cListGeometric3DObject GlobalList = new cListGeometric3DObject("Elevation Map MetaObject");

            if(this.Input!=null)
            foreach (var item in this.Input)
            {
                c3DElevationMap _3DMap = new c3DElevationMap(new cPoint3D(-this.Input[0].Count / 2, -this.Input[0][0].Count / 2, 0), item, this.LUT);
                _3DMap.SetName("Elevation Map [" + item.Name +"]");
                GlobalList.Add(_3DMap);
            }

            if (this.InputImage != null)
            {
                for (int i = 0; i < this.InputImage.GetNumChannels(); i++)
                {
                    c3DElevationMap _3DMapFromImage = new c3DElevationMap(new cPoint3D(0, 0, 0), this.InputImage, i, 0);
                    if(this.InputImage.AssociatedImagePanel!=null)
                    _3DMapFromImage.SetOpacity(this.InputImage.AssociatedImagePanel.LUTManager.GetImageDisplayProperties().ListOpacity[i]/100.0);
                    _3DMapFromImage.SetName("Elevation Map [" + this.InputImage.SingleChannelImage[i].Name+"]");
                    GlobalList.Add(_3DMapFromImage);
                }
            }

            foreach (var item in GlobalList)
            {
                MyWorld.AddGeometric3DObject(item);
            }

            MyWorld.BackGroundColor = cGlobalInfo.OptionsWindow.FFAllOptions.panelFor3DBackColor.BackColor;
            V3D.SetInputData(MyWorld);
            V3D.Run();

            #region obsolete
            //// get a reference to the renderwindow of our renderWindowControl1
            //vtkRenderWindow RenderWindow = renderWindowControl1.RenderWindow;
            //// get a reference to the renderer
            //vtkRenderer Renderer = RenderWindow.GetRenderers().GetFirstRenderer();
            //vtkPoints points = vtkPoints.New();

            //double MaxZ = this.Input.Max();
            //double MinZ = this.Input.Min();

            //for (int IdxX = 0; IdxX < this.Input.Count; IdxX++)
            //    for (int IdxY = 0; IdxY < this.Input[IdxX].Count; IdxY++)
            //    {
            //        double Value = ((this.Input[IdxX][this.Input[IdxX].Count- IdxY-1] - MinZ) / (MaxZ - MinZ) * this.Input.Count) / 5;
            //        points.InsertNextPoint(IdxX, IdxY, Value);
            //    }

            //double[] bounds = points.GetBounds();

            //// Add the grid points to a polydata object
            //vtkPolyData inputPolyData = vtkPolyData.New();
            //inputPolyData.SetPoints(points);

            //// Triangulate the grid points
            //vtkDelaunay2D delaunay = vtkDelaunay2D.New();
            //delaunay.SetInput(inputPolyData);
            //delaunay.Update();

            //vtkElevationFilter elevationFilter = vtkElevationFilter.New();
            //elevationFilter.SetInputConnection(delaunay.GetOutputPort());
            //elevationFilter.SetLowPoint(0.0, 0.0, bounds[5]);
            //elevationFilter.SetHighPoint(0.0, 0.0, bounds[4]);
            //elevationFilter.Update();

            //vtkPolyData output = vtkPolyData.New();
            //output.ShallowCopy(vtkPolyData.SafeDownCast(elevationFilter.GetOutput()));

            //// Generate the colors for each point based on the color map
            //vtkUnsignedCharArray colors = vtkUnsignedCharArray.New();
            //colors.SetNumberOfComponents(3);
            //colors.SetName("Colors");
            //output.GetPointData().AddArray(colors);

            //// Visualize
            //vtkPolyDataMapper mapper = vtkPolyDataMapper.New();
            //mapper.SetInput(output);

            //// Create the color map
            //vtkLookupTable colorLookupTable = vtkLookupTable.New();
            //colorLookupTable.Build();

            //if (LUT == null)
            //{
            //    cLUT MyLut = new cLUT();
            //    LUT = MyLut.LUT_JET;
            //}

            ////colorLookupTable.SetValueRange(1,0);//bounds[0], bounds[1]);

            //double LUTSize = LUT[0].Length;
            //colorLookupTable.SetNumberOfTableValues((int)LUTSize - 1);

            //for (int i = 0; i < (int)LUTSize - 1; i++)
            //{
            //    colorLookupTable.SetTableValue((int)LUTSize - 1 - i-1, this.LUT[0][i] / LUTSize, this.LUT[1][i] / LUTSize, this.LUT[2][i] / LUTSize, 1);
            //}

            ////colorLookupTable.SetSaturationRange(0, 0);
            ////colorLookupTable.SetTableRange(bounds[4], bounds[5]);
            ////table.SetRange(range[0], range[1]); //shoul here not be the minimum/maximum possible of "data"?
            //// colorLookupTable.SetRampToLinear();
            //colorLookupTable.Build();

            //mapper.SetLookupTable(colorLookupTable);

            //vtkActor NewActor = vtkActor.New();
            //NewActor.SetMapper(mapper);
            //Renderer.AddActor(NewActor);

            //// set background color
            //Renderer.SetBackground(BackGroundColor.R / 255.0, BackGroundColor.G / 255.0, BackGroundColor.B / 255.0);

            //// ensure all actors are visible (in this example not necessarely needed,
            //// but in case more than one actor needs to be shown it might be a good idea)
            //Renderer.ResetCamera();
            #endregion
        }
Beispiel #15
0
        public cVolumeRendering3D(cSingleChannelImage SingleChannelImage, cPoint3D Pos, byte[][] NewLUT, c3DNewWorld AssociatedWorld)
        {
            if (SingleChannelImage.Data == null) return;

            baseInit(AssociatedWorld);

            this.SetName("Volume 3D [" + SingleChannelImage.Name + "]");

            this.LUT = NewLUT;

            vtk_volume = vtkVolume.New();
            vtkImageData imageData = vtkImageData.New();
            vtkUnsignedShortArray UshortArray = vtkUnsignedShortArray.New();

            voi = vtkExtractVOI.New();
            ColorTransferFunction = vtkColorTransferFunction.New();

            for (int i = 0; i < SingleChannelImage.Width * SingleChannelImage.Height * SingleChannelImage.Depth; i++)
            {
                UshortArray.InsertTuple1(i, (ushort)SingleChannelImage.Data[i]);    // data are converted to UShort
            }

            imageData = vtkImageData.New();
            imageData.SetDimensions(SingleChannelImage.Width, SingleChannelImage.Height, SingleChannelImage.Depth);
            imageData.SetOrigin(0, 0, 0);

            if ((SingleChannelImage.Resolution.X == 0) || (SingleChannelImage.Resolution.Y == 0) || (SingleChannelImage.Resolution.Z == 0))
                imageData.SetSpacing(1.0, 1.0, 1.0);
            else
                imageData.SetSpacing(SingleChannelImage.Resolution.X, SingleChannelImage.Resolution.Y, SingleChannelImage.Resolution.Z);

            imageData.GetPointData().SetScalars(UshortArray);

            voi = vtkExtractVOI.New();
            voi.SetInput(imageData);
            voi.SetVOI(0, SingleChannelImage.Width - 1, 0, SingleChannelImage.Height - 1, 0, SingleChannelImage.Depth - 1);
            voi.SetSampleRate(1, 1, 1);

            opacityTransferFunction = vtkPiecewiseFunction.New();

            range = imageData.GetScalarRange();

            opacityTransferFunction.AddPoint(range[0], 0.0);
            opacityTransferFunction.AddPoint(range[1], 0.3);
            //opacityTransferFunction.AddPoint(2000, 0.1);
            //opacityTransferFunction.AddPoint(range[0] + (range[1]-range[0])/2.0, 0.0);
            //opacityTransferFunction.AddPoint(range[1], 0.7);

            if (LUT == null)
            {
                //cLUT MyLut = new cLUT();
                //LUT = MyLut.LUT_JET;
                ColorTransferFunction.AddRGBPoint(0, 0 , 0, 0);
                ColorTransferFunction.AddRGBPoint(1, 1, 1, 1);
            }

            //double LUTSize = LUT[0].Length;

            //for (int i = 0; i < (int)LUTSize; i++)
            //{
            //    colorTransferFunction.AddRGBPoint(i, LUT[0][i] / LUTSize, LUT[1][i] / LUTSize, LUT[2][i] / LUTSize);

            //}

            ColorTransferFunction.Build();

            volumeProperty = vtkVolumeProperty.New();
            volumeProperty.SetColor(ColorTransferFunction);

            volumeProperty.SetScalarOpacity(opacityTransferFunction);
            volumeProperty.SetInterpolationTypeToNearest();
            volumeProperty.ShadeOff();

            vtkVolumeTextureMapper3D volumeTextureMapper = vtkVolumeTextureMapper3D.New();
            volumeTextureMapper.SetInputConnection(voi.GetOutputPort());

            //vtkVolumeRayCastCompositeFunction compositeFunction = vtkVolumeRayCastCompositeFunction.New();
            //vtkVolumeRayCastMapper volumeMapper = vtkVolumeRayCastMapper.New();
            //volumeMapper.SetVolumeRayCastFunction(compositeFunction);
            //volumeMapper.SetInputConnection(voi.GetOutputPort());

            vtk_volume = vtkVolume.New();
            vtk_volume.SetMapper(volumeTextureMapper);
            vtk_volume.SetProperty(volumeProperty);
            vtk_volume.PickableOn();

            vtk_volume.SetPosition(Pos.X, Pos.Y, Pos.Z);
        }
Beispiel #16
0
        private void dRC3DToolStripMenuItem_Click(object sender, EventArgs e)
        {

            if (cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptors().Count < 3)
            {
                MessageBox.Show("At least 3 descriptors are required for this operation !", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
                return;
            }

            cListExtendedTable LET = new cListExtendedTable();

            //List<cListWells> ListWells = new List<cListWells>();
            //ListWells.Add(cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().ListActiveWells);

            // firstly, wells are grouped by class
            //foreach (var item in cGlobalInfo.ListWellClasses)
            //{
            //    List<cWellClassType> TypeForFilter = new List<cWellClassType>();
            //    TypeForFilter.Add(item);
            //    cListWells TmpListWells = cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().ListActiveWells.Filter(TypeForFilter);
            //    cGeneralDRC gDRC = new cGeneralDRC(TmpListWells);
            //    LET.Add(gDRC.ListAverageValues);
            //}


            for (int i = 0; i < 3; i++)
            {
                List<int> GroupForFilter = new List<int>();
                GroupForFilter.Add(i);
                cListWells TmpListWells = cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().ListActiveWells.FilterByGroup(GroupForFilter);
                cGeneralDRC gDRC = new cGeneralDRC(TmpListWells);
                LET.Add(gDRC.ListAverageValues);
            }



            cViewer3D V3D = new cViewer3D();
            c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));

            c3DObjectScatterPoints _3DScatterPt = new c3DObjectScatterPoints();
            //_3DScatterPt.SetInputData(cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().ListActiveWells.GetDescriptorValues(cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptors(), false));
            //  _3DScatterPt.GlobalInfo = this.GlobalInfo;
            _3DScatterPt.SetInputData(LET);
            // _3DScatterPt.IsLinked = true;
            _3DScatterPt.Run(MyWorld);

            cListGeometric3DObject GlobalList = _3DScatterPt.GetOutPut();

            foreach (var item in GlobalList)
            {
                MyWorld.AddGeometric3DObject(item);
            }


            MyWorld.BackGroundColor = cGlobalInfo.OptionsWindow.FFAllOptions.panelFor3DBackColor.BackColor;

            V3D.SetInputData(MyWorld);
            V3D.Run();

            cDisplayToWindow DTW = new cDisplayToWindow();
            DTW.SetInputData(V3D.GetOutPut());
            DTW.Title = "3D Dose Response Visualization";
            DTW.Run();
            DTW.Display();
        }
Beispiel #17
0
        private void dToolStripMenuItemScatterPlot3D_Click(object sender, EventArgs e)
        {
            int MaxNumberOfPts = (int)cGlobalInfo.OptionsWindow.FFAllOptions.numericUpDownMinNumPointForFastDisp.Value;

            if (cGlobalInfo.CurrentScreening.ListPlatesActive.GetListActiveWells().Count > MaxNumberOfPts)
            {
                cExtendedTable ET = cGlobalInfo.CurrentScreening.ListPlatesActive.GetListActiveWells().GetAverageDescriptorValues(cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptors(), false, false);
                cNormalize N = new cNormalize();
                N.SetInputData(ET);
                N.NormalizationType = eNormalizationType.MIN_MAX;
                N.Run();
                cExtendedTable NormTable = N.GetOutPut();

                cViewer3D V3D = new cViewer3D();
                c3DPointCloud _3DPtCloud = new c3DPointCloud(NormTable);
                _3DPtCloud.AutomatedPtColorMode = 1;
                _3DPtCloud.Create(new cPoint3D(0, 0, 0));
                _3DPtCloud.SetName("_3DPtCloud");
                cListGeometric3DObject GlobalList = new cListGeometric3DObject("3D Point Cloud MetaObject");

                GlobalList.Add(_3DPtCloud);

                c3DObject_Axis Axis = new c3DObject_Axis();
                cExtendedTable T = new cExtendedTable();
                T.Add(new cExtendedList(ET[0].Name));

                T[0].Tag = ET[0].Tag;
                T[0].Add(0);
                T[0].Add(1);
                T.Add(new cExtendedList(ET[1].Name));
                T[1].Tag = ET[1].Tag;
                T[1].Add(0);
                T[1].Add(1);

                if (ET.Count > 2)
                {
                    T.Add(new cExtendedList(ET[2].Name));
                    T[2].Tag = ET[2].Tag;
                    T[2].Add(0);
                    T[2].Add(1);
                }

                Axis.SetInputData(T);

                c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));
                Axis.Run(MyWorld);

                GlobalList.AddRange(Axis.GetOutPut());

                // GlobalList.Add(Axis);

                foreach (var item in GlobalList)
                {
                    MyWorld.AddGeometric3DObject(item);
                }

                //  MyWorld.BackGroundColor = cGlobalInfo.OptionsWindow.FFAllOptions.panelFor3DBackColor.BackColor;

                V3D.SetInputData(MyWorld);
                V3D.Run();

                cDisplayToWindow DTW = new cDisplayToWindow();
                DTW.SetInputData(V3D.GetOutPut());
                DTW.Title = "3D Cloud Point - " + ET[0].Count + " points";
                DTW.Run();

                DTW.Display();
            }
            else
            {
                cGlobalInfo.OptionsWindow.checkBoxConnectDRCPts.Checked = false;
                FormFor3DDataDisplay FormToDisplayXYZ = new FormFor3DDataDisplay(ProcessModeEntireScreeningToolStripMenuItem.Checked, cGlobalInfo.CurrentScreening);
                for (int i = 0; i < (int)cGlobalInfo.CurrentScreening.ListDescriptors.Count; i++)
                {
                    FormToDisplayXYZ.comboBoxDescriptorX.Items.Add(cGlobalInfo.CurrentScreening.ListDescriptors[i].GetName());
                    FormToDisplayXYZ.comboBoxDescriptorY.Items.Add(cGlobalInfo.CurrentScreening.ListDescriptors[i].GetName());
                    FormToDisplayXYZ.comboBoxDescriptorZ.Items.Add(cGlobalInfo.CurrentScreening.ListDescriptors[i].GetName());
                }
                FormToDisplayXYZ.Show();
                FormToDisplayXYZ.comboBoxDescriptorX.Text = cGlobalInfo.CurrentScreening.ListDescriptors[0].GetName() + " ";
                FormToDisplayXYZ.comboBoxDescriptorY.Text = cGlobalInfo.CurrentScreening.ListDescriptors[0].GetName() + " ";
                FormToDisplayXYZ.comboBoxDescriptorZ.Text = cGlobalInfo.CurrentScreening.ListDescriptors[0].GetName() + " ";
            }
            return;
        }
Beispiel #18
0
 void renderWindowControl1_Disposed(object sender, EventArgs e)
 {
     this.Input.Dispose();
     this.Input = null;
     GC.SuppressFinalize(this);
     GC.Collect();
 }
Beispiel #19
0
        private void spiralToolStripMenuItem_Click(object sender, EventArgs e)
        {
            // first let's define all the stimuli
            #region Build the stimuli
            cStimuli ListCellStimuli = new cStimuli();

            cStimulus_Physical Gravity = new cStimulus_Physical("Gravity");
            ListCellStimuli.Add(Gravity);
            //cStimulus_Physical WorldEdges = new cStimulus_Physical("World Edges");
            //ListCellStimuli.Add(WorldEdges);
            cStimulus_Physical BrownianMotion = new cStimulus_Physical("Brownian Motion");
            ListCellStimuli.Add(BrownianMotion);


            cStimulus_Chemical ToxicCompound1 = new cStimulus_Chemical("ToxicCompound1");
            ListCellStimuli.Add(ToxicCompound1);
            #endregion


            #region build the cell agents
            #endregion

            cNewAgent BiologicalExperiment_DRC = new cNewAgent(new cPoint3D(0, 0, 0), new cPoint3D(5, 5, 5), "DRC");

            double Concentration = 0.01;
            for (int i = 0; i < 2; i++)
            {
                double WellSpacing = 1;
                cNewAgent BiologicalExperiment_Well = new cNewAgent(new cPoint3D(WellSpacing, 0, 0), new cPoint3D(1, 1, 1), "Well " + i);

                // add a new Property to the well
                cInternalProperty Cpd1Concentration = new cInternalProperty();
                Cpd1Concentration.Name = "Compound 1 Concentration";
                BiologicalExperiment_Well.AddProperty(Cpd1Concentration);

                // add the cellular agents in the well
                int RegularCellsNumber = 20;
                for (int CellIdx = 0; CellIdx < RegularCellsNumber; CellIdx++)
                {
                    cAgent_Cell Agent_RegularCell = new cAgent_Cell(new cPoint3D(0.02 * CellIdx, 0.2, 0.0200 * i), new cPoint3D(0.0100, 0.0100, 0.0100), "Regular Cell " + CellIdx);
                    Agent_RegularCell.AssociatedStimuli = ListCellStimuli;
                    BiologicalExperiment_Well.AddNewAgent(Agent_RegularCell);
                }

                int CancerCellsNumber = 30;
                for (int CellIdx = 0; CellIdx < CancerCellsNumber; CellIdx++)
                {
                    cAgent_Cell Agent_CancerCell = new cAgent_Cell(new cPoint3D(0.0100 * i, 0.0100 * CellIdx, 0.1000), new cPoint3D(0.0200, 0.0200, 0.0200), "Cancer Cell " + CellIdx);
                    Agent_CancerCell.AssociatedStimuli = ListCellStimuli;
                    BiologicalExperiment_Well.AddNewAgent(Agent_CancerCell);
                }


                // add the well agent in the DRC
                BiologicalExperiment_DRC.AddNewAgent(BiologicalExperiment_Well);

                Concentration *= 2;
            }

            for (int Iteration = 0; Iteration < 1; Iteration++)
            {
                BiologicalExperiment_DRC.Run();
            }

            // display objects in 3D
            cViewer3D V3D = new cViewer3D();
            // c3DNewWorld MyWorld = new c3DNewWorld((cPoint3D)BiologicalExperiment_DRC.InternalProperties["Volume"], new cPoint3D(1, 1, 1));
            c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));
            V3D.SetInputData(MyWorld);
            V3D.Run();

            cDesignerSinglePanel CD = new cDesignerSinglePanel();
            CD.SetInputData(V3D.GetOutPut());
            if (CD.Run().IsSucceed == false) return;

            cListGeometric3DObject GlobalList = new cListGeometric3DObject("Global List");
            cListGeometric3DObject CellsList = new cListGeometric3DObject("Cells");

            cInternalProperty TmpProp;

            foreach (cNewAgent TmpWell in BiologicalExperiment_DRC)
            {

                cPoint3D ObjectPos = TmpWell.GetAbsoluteGetPosition();

                c3DCube SpaceCube = new c3DCube();
                TmpProp = TmpWell.InternalProperties["Volume"];
                cPoint3D VOlume = new cPoint3D(0, 0, 0);
                SpaceCube.Create(ObjectPos, VOlume, Color.Blue);
                SpaceCube.SetOpacity(0.2);
                GlobalList.AddObject(SpaceCube);

                foreach (cNewAgent TmpCell in TmpWell)
                {
                    ObjectPos = TmpCell.GetAbsoluteGetPosition();
                    c3DSphere _3DSphere = new c3DSphere(ObjectPos, 0.05, Color.Red);
                    TmpProp = TmpCell.InternalProperties["Volume"];
                    VOlume = new cPoint3D(0, 0, 0);// (cPoint3D)TmpCell.InternalProperties["Volume"];
                    //_3DSphere.(ObjectPos, 0.5, Color.Red);
                    _3DSphere.SetName(TmpCell.GetName());
                    _3DSphere.SetOpacity(1);

                    CellsList.AddObject(_3DSphere);
                }
            }


            GlobalList.AddRange(CellsList);

            foreach (var item in GlobalList)
                MyWorld.AddGeometric3DObject(item);

            cDisplayToWindow CDW = new cDisplayToWindow();
            CDW.SetInputData(CD.GetOutPut());
            CDW.Title = "3D world";
            if (CDW.Run().IsSucceed == false) return;
            CDW.Display();
            return;
        }
        public cFeedBackMessage Run()
        {
            if (base.Start() == false)
            {
                base.FeedBackMessage.IsSucceed = false;
                return base.FeedBackMessage;
            }

            if ((this.Input == null)||(this.Input.Count==0))
            {

                FeedBackMessage.IsSucceed = false;
                FeedBackMessage.Message = "No input data defined.";
                return FeedBackMessage;
            }
            FeedBackMessage.IsSucceed = true;

            #region Properties Management
            object _firstValue = base.ListProperties.FindByName("Normalized ?");
            bool IsNormalized = false;
            if (_firstValue == null)
            {
                base.GenerateError("-Normalized ?- not found !");
                return base.FeedBackMessage;
            }
            try
            {
                cProperty TmpProp = (cProperty)_firstValue;
                IsNormalized = (bool)TmpProp.GetValue();
            }
            catch (Exception)
            {
                base.GenerateError("-Normalized ?- cast didn't work");
                return base.FeedBackMessage;
            }

            _firstValue = base.ListProperties.FindByName("Draw Axis ?");
            bool IsdrawAxis = true;
            if (_firstValue == null)
            {
                base.GenerateError("-Draw Axis ?- not found !");
                return base.FeedBackMessage;
            }
            try
            {
                cProperty TmpProp = (cProperty)_firstValue;
                IsdrawAxis = (bool)TmpProp.GetValue();
            }
            catch (Exception)
            {
                base.GenerateError("-Draw Axis ?- cast didn't work");
                return base.FeedBackMessage;
            }

            _firstValue = base.ListProperties.FindByName("Link Points ?");
            bool IsLinked = false;
            if (_firstValue == null)
            {
                base.GenerateError("-Link Points ?- not found !");
                return base.FeedBackMessage;
            }
            try
            {
                cProperty TmpProp = (cProperty)_firstValue;
                IsLinked = (bool)TmpProp.GetValue();
            }
            catch (Exception)
            {
                base.GenerateError("-Link Points ?- cast didn't work");
                return base.FeedBackMessage;
            }

            _firstValue = base.ListProperties.FindByName("Desc. 1");
            string Desc1;
            if (_firstValue == null)
            {
                base.GenerateError("-Desc. 1- not found !");
                return base.FeedBackMessage;
            }
            try
            {
                cProperty TmpProp = (cProperty)_firstValue;
                Desc1 = (string)TmpProp.GetValue();
            }
            catch (Exception)
            {
                base.GenerateError("-Desc. 1- cast didn't work");
                return base.FeedBackMessage;
            }
            cDescriptorType DescX = cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorByName(Desc1);
            if (DescX == null)
            {
                base.GenerateError(Desc1 + " is not a descriptor !");
                return base.FeedBackMessage;
            }

            _firstValue = base.ListProperties.FindByName("Desc. 2");
            if (_firstValue == null)
            {
                base.GenerateError("-Desc. 2- not found !");
                return base.FeedBackMessage;
            }
            try
            {
                cProperty TmpProp = (cProperty)_firstValue;
                Desc1 = (string)TmpProp.GetValue();
            }
            catch (Exception)
            {
                base.GenerateError("-Desc. 2- cast didn't work");
                return base.FeedBackMessage;
            }
            cDescriptorType DescY = cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorByName(Desc1);
            if (DescY == null)
            {
                base.GenerateError(Desc1 + " is not a descriptor !");
                return base.FeedBackMessage;
            }

            _firstValue = base.ListProperties.FindByName("Desc. 3");
            if (_firstValue == null)
            {
                base.GenerateError("-Desc. 3- not found !");
                return base.FeedBackMessage;
            }
            try
            {
                cProperty TmpProp = (cProperty)_firstValue;
                Desc1 = (string)TmpProp.GetValue();
            }
            catch (Exception)
            {
                base.GenerateError("-Desc. 2- cast didn't work");
                return base.FeedBackMessage;
            }
            cDescriptorType DescZ = cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorByName(Desc1);
            if (DescZ == null)
            {
                base.GenerateError(Desc1 + " is not a descriptor !");
                return base.FeedBackMessage;
            }

            #endregion

            List<cDescriptorType> ListDesc = new List<cDescriptorType>();
            ListDesc.Add(DescX);
            ListDesc.Add(DescY);
            ListDesc.Add(DescZ);

            cListExtendedTable LET = new cListExtendedTable();
            foreach (var item in cGlobalInfo.ListWellClasses)
            {
                List<cWellClassType> TypeForFilter = new List<cWellClassType>();
                TypeForFilter.Add(item);

                cExtendedTable TmpTable = ((cListWells)this.Input.Filter(TypeForFilter)).GetAverageDescriptorValues(ListDesc,false, false);
                if (TmpTable != null)
                    LET.Add(TmpTable);
            }

            cViewer3D V3D = new cViewer3D();
            c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));

            c3DObjectScatterPoints _3DScatterPt = new c3DObjectScatterPoints();

            _3DScatterPt.ListProperties.FindByName("Draw Axis ?").SetNewValue(IsdrawAxis);
            _3DScatterPt.ListProperties.FindByName("Normalized ?").SetNewValue(IsNormalized);
            _3DScatterPt.ListProperties.FindByName("Link Points ?").SetNewValue(IsLinked);
            _3DScatterPt.SetInputData(LET);
            if (_3DScatterPt.Run(MyWorld).IsSucceed == false) return base.FeedBackMessage;

            cListGeometric3DObject GlobalList = _3DScatterPt.GetOutPut();

            foreach (var item in GlobalList)
            {
                MyWorld.AddGeometric3DObject(item);
            }

            MyWorld.BackGroundColor = cGlobalInfo.OptionsWindow.FFAllOptions.panelFor3DBackColor.BackColor;

            V3D.SetInputData(MyWorld);
            V3D.Run();

            cDisplayToWindow DTW = new cDisplayToWindow();
            DTW.SetInputData(V3D.GetOutPut());
               DTW.Title = "3D Scatter Plot(List "+this.Input.Count +" Wells)";
            DTW.Run();

            DTW.Display();

            return base.FeedBackMessage;
        }
Beispiel #21
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();
        }
Beispiel #22
0
        private void ToolStripMenuItem_3DTest(object sender, EventArgs e)
        {
            Plugin3D NewPlug = new Plugin3D(this.AssociatedImage);
            NewPlug.Show();

            return;

            c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(this.AssociatedImage.Width, this.AssociatedImage.Height, this.AssociatedImage.Depth),
                                                    new cPoint3D(1, 1, 1));

            cVolumeDetection Detection = new cVolumeDetection(this.AssociatedImage, 2, false);
            Detection.SetShift(new cPoint3D(0, 0, 0));
            Detection.SetContainers(null);

            List<cInteractive3DObject> AssociatedBiologicalObjectList = Detection.IntensityThreshold(150f,
                                         10,
                                         float.MaxValue);

            for (int i = 0; i < AssociatedBiologicalObjectList.Count; i++)
            {
                cBiological3DVolume TmpVol = (cBiological3DVolume)AssociatedBiologicalObjectList[i];

                // MyWorld.AddGeometric3DObject(TmpVol.AttachText("Object " + i, 5, Color.White));

                //    //if (Obj.checkIsBoxPointingArrow.Checked)
                cGeometric3DObject AssociatedArrow = TmpVol.AttachPointingArrow(5f, Color.Tomato);
                MyWorld.AddGeometric3DObject(AssociatedArrow);

                AssociatedBiologicalObjectList[i].SetOpacity(/*(double)Obj.ColorOpacity.numericUpDownValue.Value*/0.5);
                AssociatedBiologicalObjectList[i].Colour = Color.Red;

                MyWorld.AddBiological3DObject(AssociatedBiologicalObjectList[i]);

            }

            MyWorld.AddVolume3D(new cVolumeRendering3D(this.AssociatedImage.SingleChannelImage[0], new cPoint3D(0, 0, 0), null, MyWorld));

            MyWorld.BackGroundColor = Color.LightGray;// GhostWhite;

            cViewer3D V3D = new cViewer3D();
            V3D.SetInputData(MyWorld);
            V3D.Run();

            cDisplayToWindow DTW = new cDisplayToWindow();
            DTW.SetInputData(V3D.GetOutPut());
            DTW.Run();
            DTW.Display();
        }