OTS/OTSIncAMeasureApp/0-OTSModel/OTSDataType/COTSField.cs

using OTSCLRINTERFACE;
using OTSMeasureApp._0_OTSModel.OTSDataType;
using OTSModelSharp;
using OTSModelSharp.ServiceCenter;
using System;
using System.Collections.Generic;
using System.Drawing;
using System.Linq;
using System.Xml;

namespace OTSDataType
{
    public class COTSField : ISlo
    {
        public COTSField leftField = null;
        public COTSField upField = null;
        public COTSField downField = null;
        public COTSField rightField = null;

        public List<CBSEImgClr> particleImages = new List<CBSEImgClr>();
        protected NLog.Logger log;
        // ID
        int m_nID;

        int measureSequence;

        // position (from field center manager) 
        protected System.Drawing.PointF m_otsPos;

        protected CBSEImgClr m_pBSEImg;

        protected double m_pixelSize;

        protected CImageHandler m_ImagePro;

        protected List<COTSParticleClr> m_listAllParticles = new List<COTSParticleClr>();//hold up all the particles abstracted from bse image;

        protected List<COTSParticleClr> m_listAnalysisParticles = new List<COTSParticleClr>();// according to xraylimit constraint,pick out the first big particles.

        protected List<COTSParticleClr> m_listXrayParticles = new List<COTSParticleClr>();//hold up all the particles that needing the xray data.


        private int imgheight;

        private int imgwidth;

        private COTSRect m_otsRect;

        private COTSSample m_sample;
        public COTSField()
        {
            log = NLog.LogManager.GetCurrentClassLogger();
            Init();
        }//only using in xmlserialization 

        public int ImgHeight { get => imgheight; set => imgheight = value; }
        public int ImgWidth { get => imgwidth; set => imgwidth = value; }
        public COTSSample Sample { get => m_sample; set => m_sample = value; }

        internal COTSRect GetOTSRect()
        {
            return m_otsRect;
        }

        internal void SetOTSRect(COTSRect value)
        {
            m_otsRect = value;
        }

        public int GetMeasureSequence()
        {
            return measureSequence;
        }

        public void SetMeasureSequence(int value)
        {
            measureSequence = value;
        }

        public List<string> strKeyName;

        public bool GetIsMeasureComplete()
        {
            return isMeasureComplete;
        }

        public void SetIsMeasureComplete(bool value)
        {
            isMeasureComplete = value;
        }

        private bool isMeasureComplete;

        public PointF GetSemPos()
        {
            return m_semPos;
        }

        public void SetSemPos(PointF value)
        {
            m_semPos = value;
        }

        private PointF m_semPos;
        public List<COTSParticleClr> GetAllParticles()
        {
            return m_listAllParticles;
        }
        public List<COTSParticleClr> GetListAnalysisParticles()
        {
            return m_listAnalysisParticles;
        }
        public List<COTSParticleClr> GetListXrayParticles()
        {
            m_listXrayParticles.Clear();
            foreach (var p in m_listAnalysisParticles)
            {
                if (p.IsXrayParticle())
                {
                    m_listXrayParticles.Add(p);


                }
            }
            return m_listXrayParticles;
        }
        public void SetListAnalysisParticles(List<COTSParticleClr> value)
        {
            m_listAnalysisParticles = value;
        }



        public COTSField(PointF centerPoint, double a_dPixelSize)
        {
            log = NLog.LogManager.GetCurrentClassLogger();
            Init();
            //m_pBSEImg = a_pBSEImg;
            m_otsPos = centerPoint;
            m_pixelSize = a_dPixelSize;


        }
        public double GetPixelSize()
        {
            return m_pixelSize;
        }
        public void SetPixelSize(double size)
        {
            m_pixelSize = size;
        }

        // initialization
        void Init()
        {
            // initialization
            m_nID = -1;
            m_otsPos = new System.Drawing.Point(0, 0);
            m_listAllParticles.Clear();
        }


        public COTSField(COTSField a_poSource)
        {

            // can't copy itself
            if (a_poSource == this)
            {
                return;
            }
            Duplicate(a_poSource);

        }
        public CBSEImgClr GetBSEImage()
        {
            return m_pBSEImg;
        }
        public Bitmap GetAnalysisParticleBlackColoredImage()
        {
            CImageHandler imghandler = new CImageHandler();
            List<COTSParticleClr> Parts = GetAllParticles();
            Bitmap img = new Bitmap(this.ImgWidth, this.ImgHeight);
            var imgparam = m_sample.GetMsrParams().GetImageProcessParam();
            var pixelsize = m_sample.CalculatePixelSize();
            imghandler.GetImageWithBlackColoredParts(Parts,imgparam,pixelsize, ref img);
            return img;
        }
        public Bitmap GetAnalysisParticleSTDColoredImage()
        {
            CImageHandler imghandler = new CImageHandler();
            List<COTSParticleClr> Parts = GetListAnalysisParticles();
            Bitmap img = new Bitmap(this.ImgWidth, this.ImgHeight);
            var imgparam = m_sample.GetMsrParams().GetImageProcessParam();
            var pixelsize = m_sample.CalculatePixelSize();
            imghandler.GetImageWithSTDColoredParts(Parts, imgparam, pixelsize, ref img);
            return img;
        }
        public void SetBSEImage(CBSEImgClr a_pBSEImg)
        {
            if (a_pBSEImg == null)
            {
                // invalid BSE image.
                log.Error("SetBSEImage: invalid BSE image.");
                return;
            }
            m_pBSEImg = a_pBSEImg;
            imgwidth = a_pBSEImg.GetWidth();
            imgheight = a_pBSEImg.GetHeight();
        }
        public void GetOriginalParticles(CSampleParam pMsrParam, double pixelsize)
        {

            // get image process parameter
            //CSampleParam pMsrParam = m_Sample.GetMsrParams();
            COTSImageProcParam pImgProcessParam = pMsrParam.GetImageProcessParam();
            var specialPartsparam = pMsrParam.GetSpecialGrayRangeParam();

            if (specialPartsparam != null && specialPartsparam.GetIsToRun())
            {
                List<CSpecialGrayRange> ranges = specialPartsparam.GetSpecialGreyRanges();
                foreach (var grayRange in ranges)
                {
                    CIntRangeClr range = new CIntRangeClr(grayRange.range.GetStart(), grayRange.range.GetEnd());
                    CDoubleRangeClr diaRange = new CDoubleRangeClr(grayRange.diameterRange.GetStart(), grayRange.diameterRange.GetEnd());
                    GetPartsBySpecialGray(range, diaRange, pixelsize, grayRange.ifCollectXray);
                }
            }
          
            // remove BES image background
            RemoveImgBGAndGetParticles(pImgProcessParam, pixelsize);

            log.Info("Find all particle num:" + GetAllParticles().Count);

            return;
        }

        private void RemoveImgBGAndGetParticles(COTSImageProcParam a_pImageProcessParam, double a_pixelSize)
        {
            if (m_pBSEImg == null)
                return;
            CImageHandler imghandler = new CImageHandler();
            List<COTSParticleClr> allParts = new List<COTSParticleClr>();
            imghandler.RemoveBGAndGetParts(this, a_pImageProcessParam, ref allParts);

            m_listAllParticles = allParts;
            return;
        }
        class particleCompOnArea : IComparer<COTSParticleClr>
        {
            public int Compare(COTSParticleClr x, COTSParticleClr y)
            {
                return y.GetActualArea().CompareTo(x.GetActualArea());//descending sort
            }
        }
        public void FilterParticles(COTSXRayParam pXRayParam)
        {
       
        log.Info("filter particle according to xraylimit");
           
           m_listAllParticles.Sort(new particleCompOnArea());



            var listXray1 = new List<COTSParticleClr>();
           
            if (m_listAllParticles.Count > pXRayParam.GetXrayLimit())
            {
                
                for (var i = 0; i < pXRayParam.GetXrayLimit(); i++)
                {
                    var part = m_listAllParticles[i];
                    int l=0, r=0, t=0, b=0;
                    part.GetOTSRect(ref l, ref t,ref r, ref b);
                    COTSRect otsrec = new COTSRect(l, t, r, b);
                    PointF p1 = otsrec.GetCenterPoint();

                    if (m_sample.IsThisPointInMeasureArea(new Point((int)p1.X, (int)p1.Y)))
                    {
                        listXray1.Add(m_listAllParticles[i]);
                    }
                   
                }

            }
            else
            {
                foreach (var p in m_listAllParticles)
                {
                    var part = p;
                    int l = 0, r = 0, t = 0, b = 0;
                    part.GetOTSRect(ref l, ref t, ref r, ref b);
                    COTSRect otsrec = new COTSRect(l, t, r, b);
                    PointF p1 = otsrec.GetCenterPoint();
                    if (m_sample.IsThisPointInMeasureArea(new Point((int)p1.X, (int)p1.Y)))
                    {
                        listXray1.Add(p);
                    }
                }
               
            }

            SetListAnalysisParticles(listXray1);

            log.Info("Xray Analysis particles:" + listXray1.Count);


        }
        public void SelectParticlesAccordingImgProp(COTSImageProcParam a_pImageProcessParam)
        {
            var selconditiondic = a_pImageProcessParam.GetParticleSelConditionDic();
            var listselparts = new List<COTSParticleClr>();
            var excludeparts = new List<COTSParticleClr>();
            if (selconditiondic.ContainsKey("dmax"))
            {
                log.Info("Select particles according to dmax");
                var rng = selconditiondic["dmax"];
                foreach (var p in GetListAnalysisParticles())
                {
                    if (p.GetDMAX() < rng.GetStart() || p.GetDMAX() >= rng.GetEnd())
                    {
                        excludeparts.Add(p);
                    }
                    else
                    {
                        log.Info("dmax=" + p.GetDMAX().ToString("F2"));
                    }

                }

            }
            if (selconditiondic.ContainsKey("dmin"))
            {
                log.Info("Select particles according to dmin");
                var rng = selconditiondic["dmin"];
                foreach (var p in GetListAnalysisParticles())
                {
                    if (p.GetDMIN() < rng.GetStart() || p.GetDMIN() >= rng.GetEnd())
                    {
                        if (!excludeparts.Contains(p))
                        {
                            excludeparts.Add(p);
                        }
                        else
                        {
                            log.Info("dmin=" + p.GetDMIN().ToString("F2"));
                        }
                    }

                }

            }
            if (selconditiondic.ContainsKey("orientation"))
            {
                log.Info("Select particles according to orientation");
                var rng = selconditiondic["orientation"];
                foreach (var p in GetListAnalysisParticles())
                {
                    if (p.GetORIENTATION() < rng.GetStart() || p.GetORIENTATION() >= rng.GetEnd())
                    {
                        if (!excludeparts.Contains(p))
                        {
                            excludeparts.Add(p);
                        }
                        else
                        {
                            log.Info("orientation=" + p.GetORIENTATION().ToString("F2"));
                        }

                    }


                }

            }
            if (selconditiondic.ContainsKey("aspect"))
            {
                log.Info("Select particles according to aspect");
                var rng = selconditiondic["aspect"];
                foreach (var p in GetListAnalysisParticles())
                {
                    double aspect = p.GetDMAX() / p.GetDMIN();
                    if (aspect < rng.GetStart() || aspect >= rng.GetEnd())
                    {
                        if (!excludeparts.Contains(p))
                        {
                            excludeparts.Add(p);
                        }
                        else
                        {
                            log.Info("aspect=" + aspect.ToString("F2"));
                        }

                    }


                }

            }
            if (selconditiondic.ContainsKey("ferret"))
            {
                log.Info("Select particles according to ferret");
                var rng = selconditiondic["ferret"];
                foreach (var p in GetListAnalysisParticles())
                {
                    double dferet = p.GetFeretDiameter();
                    if (dferet < rng.GetStart() || dferet >= rng.GetEnd())
                    {
                        if (!excludeparts.Contains(p))
                        {
                            excludeparts.Add(p);
                        }
                        else
                        {
                            log.Info("ferret=" + dferet.ToString("F2"));
                        }

                    }

                }

            }

            foreach (var p in GetListAnalysisParticles())
            {
                if (!excludeparts.Contains(p))
                {
                    listselparts.Add(p);
                }

            }


            SetListAnalysisParticles(listselparts);

            log.Info("Analysis particles:" + listselparts.Count);


        }
        public void RemoveDuplicateOverlapParticles(int overlap)
        {
            List<COTSParticleClr> finalparts = new List<COTSParticleClr>();
            List<COTSParticleClr> duplicateparts = new List<COTSParticleClr>();
            //find left side duplicate particles
            var leftparts = this.GetSideParticlesByOverlap(SORTING_DIRECTION.LEFT, overlap);
            if (leftField != null && leftField.measureSequence < this.measureSequence)
            {
                var rightsideparts = leftField.GetSideParticlesByOverlap(SORTING_DIRECTION.RIGHT, overlap);
                if (leftField.upField != null && leftField.upField.measureSequence < this.measureSequence)//include the left up corner parts
                {
                    var leftupParts = leftField.upField.GetSideParticlesByOverlap(SORTING_DIRECTION.RIGHT, overlap);
                    rightsideparts.AddRange(leftupParts);
                }
                if (leftField.downField != null && leftField.downField.measureSequence < this.measureSequence)//include the left down corner parts
                {
                    var leftdownParts = leftField.downField.GetSideParticlesByOverlap(SORTING_DIRECTION.RIGHT, overlap);
                    rightsideparts.AddRange(leftdownParts);
                }

                log.Info("left side particles num:" + leftparts.Count.ToString());
                foreach (var p in leftparts)
                {
                    int pleft = 0, pright = 0, ptop = 0, pbottom = 0;
                    p.GetOTSRect(ref pleft, ref ptop, ref pright, ref pbottom);
                    COTSRect prec = new COTSRect(pleft, ptop, pright, pbottom);
                    PointF pcenter = prec.GetCenterPoint();

                    foreach (var p1 in rightsideparts)
                    {
                        int p1left = 0, p1right = 0, p1top = 0, p1bottom = 0;
                        p1.GetOTSRect(ref p1left, ref p1top, ref p1right, ref p1bottom);
                        COTSRect p1rec = new COTSRect(p1left, p1top, p1right, p1bottom);
                        PointF p1Center = p1rec.GetCenterPoint();
                        if (Math.Abs(pcenter.X - p1Center.X) < 2 * overlap && Math.Abs(pcenter.Y - p1Center.Y) < 2 * overlap)
                        {
                            var sim = p.CalculateSimilarity(p1);
                            if (sim > 0.95)
                            {
                                log.Warn("remove left side duplicate particle,similarity:" + sim.ToString("F3"));
                                log.Warn("P1:" + p.GetImgPortraitString());
                                log.Warn("P2:" + p1.GetImgPortraitString());                              
                                duplicateparts.Add(p);
                                break;
                            }
                        }

                    }



                }
            }

            //find up side duplicate particles
            var upparts = this.GetSideParticlesByOverlap(SORTING_DIRECTION.UP, overlap);
            if (upField != null && upField.measureSequence < this.measureSequence)
            {

                var othersideparts = upField.GetSideParticlesByOverlap(SORTING_DIRECTION.DOWN, overlap);


                log.Info("up side particles num:" + upparts.Count.ToString());
                foreach (var p in upparts)
                {
                    int pleft = 0, pright = 0, ptop = 0, pbottom = 0;
                    p.GetOTSRect(ref pleft, ref ptop, ref pright, ref pbottom);
                    COTSRect prec = new COTSRect(pleft, ptop, pright, pbottom);
                    PointF pcenter = prec.GetCenterPoint();


                    foreach (var p1 in othersideparts)
                    {
                        int p1left = 0, p1right = 0, p1top = 0, p1bottom = 0;
                        p1.GetOTSRect(ref p1left, ref p1top, ref p1right, ref p1bottom);
                        COTSRect p1rec = new COTSRect(p1left, p1top, p1right, p1bottom);
                        PointF p1Center = p1rec.GetCenterPoint();
                        if (Math.Abs(pcenter.X - p1Center.X) < 2 * overlap && Math.Abs(pcenter.Y - p1Center.Y) < 2 * overlap)
                        {
                            var sim = p.CalculateSimilarity(p1);
                            if (sim > 0.95)
                            {
                                log.Warn("remove upside duplicate particle,similarity:" + sim.ToString("F3"));
                                log.Warn("P1:" + p.GetImgPortraitString());
                                log.Warn("P2:" + p1.GetImgPortraitString());

                                duplicateparts.Add(p);
                                break;
                            }
                        }

                    }



                }
            }



            //find right side duplicate particles
            var rightparts = this.GetSideParticlesByOverlap(SORTING_DIRECTION.RIGHT, overlap);
            if (rightField != null && rightField.measureSequence < this.measureSequence)
            {
                log.Info("right side particles num:" + rightparts.Count.ToString());
                var othersideparts = rightField.GetSideParticlesByOverlap(SORTING_DIRECTION.LEFT, overlap);
                if (rightField.upField != null && rightField.upField.measureSequence < this.measureSequence)// right up corner parts
                {
                    var rightupParts = rightField.upField.GetSideParticlesByOverlap(SORTING_DIRECTION.LEFT, overlap);
                    othersideparts.AddRange(rightupParts);
                }
                if (rightField.downField != null && leftField.downField.measureSequence < this.measureSequence)// rightdown corner parts
                {
                    var rightdownParts = leftField.downField.GetSideParticlesByOverlap(SORTING_DIRECTION.LEFT, overlap);
                    othersideparts.AddRange(rightdownParts);
                }

                foreach (var p in rightparts)
                {
                    int pleft = 0, pright = 0, ptop = 0, pbottom = 0;
                    p.GetOTSRect(ref pleft, ref ptop, ref pright, ref pbottom);
                    COTSRect prec = new COTSRect(pleft, ptop, pright, pbottom);
                    PointF pcenter = prec.GetCenterPoint();

                    foreach (var p1 in othersideparts)
                    {
                        int p1left = 0, p1right = 0, p1top = 0, p1bottom = 0;
                        p1.GetOTSRect(ref p1left, ref p1top, ref p1right, ref p1bottom);
                        COTSRect p1rec = new COTSRect(p1left, p1top, p1right, p1bottom);
                        PointF p1Center = p1rec.GetCenterPoint();
                        if (Math.Abs(pcenter.X - p1Center.X) < 2 * overlap && Math.Abs(pcenter.Y - p1Center.Y) < 2 * overlap)
                        {
                            var sim = p.CalculateSimilarity(p1);
                            if (sim > 0.95)
                            {
                                log.Warn("remove right side duplicate particle,similarity:" + sim.ToString("F3"));
                                log.Warn("P1:" + p.GetImgPortraitString());
                                log.Warn("P2:" + p1.GetImgPortraitString());
                                duplicateparts.Add(p);
                                break;
                            }
                        }

                    }

                }
            }



            //find down side duplicate particles
            var downparts = this.GetSideParticlesByOverlap(SORTING_DIRECTION.DOWN, overlap);
            if (downField != null && downField.measureSequence < this.measureSequence)
            {

                log.Info("down side particles num:" + downparts.Count.ToString());
                var othersideparts = downField.GetSideParticlesByOverlap(SORTING_DIRECTION.UP, overlap);
                foreach (var p in downparts)
                {
                    int pleft = 0, pright = 0, ptop = 0, pbottom = 0;
                    p.GetOTSRect(ref pleft, ref ptop, ref pright, ref pbottom);
                    COTSRect prec = new COTSRect(pleft, ptop, pright, pbottom);
                    PointF pcenter = prec.GetCenterPoint();

                    foreach (var p1 in othersideparts)
                    {
                        int p1left = 0, p1right = 0, p1top = 0, p1bottom = 0;
                        p1.GetOTSRect(ref p1left, ref p1top, ref p1right, ref p1bottom);
                        COTSRect p1rec = new COTSRect(p1left, p1top, p1right, p1bottom);
                        PointF p1Center = p1rec.GetCenterPoint();
                        if (Math.Abs(pcenter.X - p1Center.X) < 2 * overlap && Math.Abs(pcenter.Y - p1Center.Y) < 2 * overlap)
                        {
                            var sim = p.CalculateSimilarity(p1);
                            if (sim > 0.95)
                            {
                                log.Warn("remove down side duplicate particle,similarity:" + sim.ToString("F3"));
                                log.Warn("P1:" + p.GetImgPortraitString());
                                log.Warn("P2:" + p1.GetImgPortraitString());
                                duplicateparts.Add(p);

                                break;
                            }
                        }

                    }

                }
            }


            foreach (var p in leftparts)
            {
                if (duplicateparts.Contains(p))
                {
                    continue;
                }
                if (!finalparts.Contains(p))
                {
                    finalparts.Add(p);
                }
            }
            foreach (var p in upparts)
            {
                if (duplicateparts.Contains(p))
                {
                    continue;
                }
                if (!finalparts.Contains(p))
                {
                    finalparts.Add(p);
                }
            }
            foreach (var p in rightparts)
            {
                if (duplicateparts.Contains(p))
                {
                    continue;
                }
                if (!finalparts.Contains(p))
                {
                    finalparts.Add(p);
                }
            }
            foreach (var p in downparts)
            {
                if (duplicateparts.Contains(p))
                {
                    continue;
                }
                if (!finalparts.Contains(p))
                {
                    finalparts.Add(p);
                }
            }


            foreach (var p in this.GetSideParticlesByOverlap(SORTING_DIRECTION.CENTER, overlap))
            {
                if (!finalparts.Contains(p))
                {
                    finalparts.Add(p);
                }
            }

            this.SetListAnalysisParticles(finalparts);
            log.Info("removing duplicate particles result:" + finalparts.Count);
        }
        private List<COTSParticleClr> GetSideParticlesByOverlap(SORTING_DIRECTION direction, int overlap)
        {
            List<COTSParticleClr> sideparts = new List<COTSParticleClr>();
            var borderedparts = this.GetBorderedParticles();
            if (direction == SORTING_DIRECTION.LEFT)
            {
                
                foreach (var p in this.GetListAnalysisParticles())
                {
                    int left = 0, top = 0, right = 0, bottom = 0;
                    p.GetOTSRect(ref left, ref top, ref right, ref bottom);

                    if (Math.Abs(right - this.GetOTSRect().GetTopLeft().X) < 2 * overlap)
                    {
                        if (!borderedparts.Contains(p) || Math.Abs(left - right) > 2 * overlap)//not on the border or it's a big particle
                        {
                            sideparts.Add(p);
                        }

                    }

                }

            }
            if (direction == SORTING_DIRECTION.RIGHT)
            {
                
                foreach (var p in this.GetListAnalysisParticles())
                {
                    int left = 0, top = 0, right = 0, bottom = 0;
                    p.GetOTSRect(ref left, ref top, ref right, ref bottom);
                    if (Math.Abs(this.GetOTSRect().GetBottomRight().X - left) < 2 * overlap)
                    {
                        if (!borderedparts.Contains(p) || Math.Abs(left - right) > 2 * overlap)//not on the border or is a big part
                        {
                            sideparts.Add(p);
                        }
                    }

                }

            }
            if (direction == SORTING_DIRECTION.UP)
            {
               
                foreach (var p in this.GetListAnalysisParticles())
                {
                    int left = 0, top = 0, right = 0, bottom = 0;
                    p.GetOTSRect(ref left, ref top, ref right, ref bottom);
                    if (Math.Abs(this.GetOTSRect().GetTopLeft().Y - bottom) < 2 * overlap)
                    {
                        if (!borderedparts.Contains(p) || Math.Abs(top - bottom) > 2 * overlap)//not on the border
                        {
                            sideparts.Add(p);
                        }
                    }

                }

            }
            if (direction == SORTING_DIRECTION.DOWN)
            {
               
                foreach (var p in this.GetListAnalysisParticles())
                {
                    int left = 0, top = 0, right = 0, bottom = 0;
                    p.GetOTSRect(ref left, ref top, ref right, ref bottom);
                    if (Math.Abs(top - this.GetOTSRect().GetBottomRight().Y) < 2 * overlap)
                    {
                        if (!borderedparts.Contains(p) || Math.Abs(top - bottom) > 2 * overlap)//not on the border
                        {
                            sideparts.Add(p);
                        }
                    }

                }

            }
            if (direction == SORTING_DIRECTION.CENTER)
            {
                foreach (var p in this.GetListAnalysisParticles())
                {
                    int left = 0, top = 0, right = 0, bottom = 0;
                    p.GetOTSRect(ref left, ref top, ref right, ref bottom);
                    var fldrec = this.GetOTSRect();
                    int fldleft = (int)fldrec.GetTopLeft().X;
                    int fldright = (int)fldrec.GetBottomRight().X;
                    int fldtop = (int)fldrec.GetTopLeft().Y;
                    int fldbottom = (int)fldrec.GetBottomRight().Y;
                    if ((Math.Abs(top - fldtop) > 2 * overlap) && (Math.Abs(fldbottom - bottom) > 2 * overlap) && (Math.Abs(left - fldleft) > 2 * overlap) && (Math.Abs(fldright - right) > 2 * overlap))
                    {
                        sideparts.Add(p);
                    }

                }

            }
            return sideparts;

        }
        public void GetPartsBySpecialGray(CIntRangeClr grayRange, CDoubleRangeClr diameterRange, double pixelSize, bool ifXray)
        {
            if (m_pBSEImg == null)
                return;
            CImageHandler imghandler = new CImageHandler();
            List<COTSParticleClr> specialParts = new List<COTSParticleClr>();
            imghandler.GetParticlesBySpecialGray(m_pBSEImg, grayRange, diameterRange, pixelSize, ref specialParts);
            foreach (var p in specialParts)
            {
                p.SetIsXrayParticle(ifXray);
                m_listAllParticles.Add(p);

            }

            return;
        }
        public bool CalParticleImageProp(List<COTSParticleClr> particles)
        {
            m_ImagePro = new CImageHandler();
            foreach (COTSParticleClr part in particles)
            {

                m_ImagePro.CalParticleImageProp(part, m_pixelSize);
            }
            return true;
        }
        public void CalculateParticleAbsolutPos(CSEMStageData pCSEMStageData)
        {
            //double dPixelSize = m_Sample.CalculatePixelSize();
            //CSEMStageData pCSEMStageData = m_pMsrThread.GetProjResultData().GetSEMStageData();
            foreach (var p in GetListAnalysisParticles())
            {

                //Point fldOtsPos = new Point((curFldData.OTSPos.X, curFldData.OTSPos.Y);
                PointF semP = new PointF(); ;
                Point semPos = new Point();
                pCSEMStageData.ConvertOTSToSEMCoord(GetOTSPosition(), ref semP);
                semPos.X = (int)semP.X;
                semPos.Y = (int)semP.Y;
                p.SetSEMPos(semPos);
            }

        }
        public void InitParticles(COTSImageProcParam a_pImageProcessParam)
        {

            // get area range
            CDoubleRange oAreaRange = a_pImageProcessParam.GetIncAreaRange();
            double rMin = oAreaRange.GetStart() / 2.0;
            double rMax = oAreaRange.GetEnd() / 2.0;

            int nTagId = 0;

            foreach (COTSParticleClr pParticle in m_listAnalysisParticles)//m_listAllParticles memorize all the particles .
            {

                pParticle.SetParticleId(nTagId);//give all the conforming particles a unified sequence no.

                pParticle.SetFieldId(GetId());

                pParticle.SetType((int)otsdataconst.OTS_PARTICLE_TYPE.NO_ANALYSIS_X_RAY);
                pParticle.SetTypeName("Not Identified");

                pParticle.SetAnalysisId(nTagId); // the same as the tagId no use now.  
                nTagId++;


            }
            log.Info("Total analysis Particles: (>" + rMin.ToString("f2") + "): " + "<" + rMax.ToString("f2") + "): " + m_listAnalysisParticles.Count);




        }

        public bool CreateXrayList(List<COTSParticleClr> a_listParticles)
        {

            foreach (COTSParticleClr pPart in a_listParticles)
            {

                System.Drawing.Point poi = (System.Drawing.Point)pPart.GetXRayPos();

                CPosXrayClr pPosXray = new CPosXrayClr();

                pPosXray.SetPosition(poi);

                pPosXray.SetPartTagId(pPart.GetParticleId());

                pPosXray.SetIndex(pPart.GetAnalysisId());

                pPosXray.SetScanFieldId(pPart.GetFieldId());

                pPart.SetXray(pPosXray);
            }
            return true;
        }
       

        public void ClearAllMeausredData()
        {
            m_listAllParticles.Clear();
            m_listAnalysisParticles.Clear();
            m_listXrayParticles.Clear();
            m_pBSEImg = null;

        }
        public bool PositionEquals(COTSField a_oSource)
        {


            if (a_oSource.m_otsPos == this.m_otsPos)
            {
                return true;
            }
            else
            {
                return false;
            }



        }



        // ID
        public int GetId()
        {
            return m_nID;
        }

        public void SetId(int a_nID)
        {
            m_nID = a_nID;
        }

        // position (from field center manager) 
        public System.Drawing.PointF GetOTSPosition()
        {
            return m_otsPos;
        }

        public void SetOTSPosition(System.Drawing.PointF a_poiPos)
        {
            m_otsPos = a_poiPos;
        }

        public List<COTSParticleClr> GetTopBorderedParticles()
        {
            List<COTSParticleClr> parts = new List<COTSParticleClr>();
            foreach (var p in m_listAnalysisParticles)
            {

                var segs = p.GetFeature().GetSegmentsList();//COTSSegment
                foreach (var seg in segs)
                {
                    if (seg.GetHeight() == 0)
                    {
                        parts.Add(p);
                        break;
                    }
                }
            }
            return parts;
        }

        public List<COTSParticleClr> GetBottomBorderedParticles()
        {
            List<COTSParticleClr> parts = new List<COTSParticleClr>();
            foreach (var p in m_listAnalysisParticles)
            {
                var segs = p.GetFeature().GetSegmentsList();
                foreach (var seg in segs)
                {
                    if (seg.GetHeight() == this.ImgHeight - 1)//the lowest height is 767(height-1),cause starting from 0.
                    {
                        parts.Add(p);
                        break;
                    }

                }
            }
            return parts;
        }
        public List<COTSParticleClr> GetBorderedParticles()
        {
            List<COTSParticleClr> parts = new List<COTSParticleClr>();
            var leftparts = this.GetLeftBorderedParticles();
            var rightp = this.GetRightBorderedParticles();
            var topp = this.GetTopBorderedParticles();
            var bottomp = this.GetBottomBorderedParticles();
            foreach (var p in leftparts)
            {
                if (!parts.Contains(p))
                {
                    parts.Add(p);
                }
            }
            foreach (var p in rightp)//
            {
                if (!parts.Contains(p))
                {
                    parts.Add(p);
                }
            }
            foreach (var p in topp)
            {
                if (!parts.Contains(p))//there may be some particles connect to both the left and top.
                {
                    parts.Add(p);
                }
            }
            foreach (var p in bottomp)
            {
                if (!parts.Contains(p))
                {
                    parts.Add(p);
                }
            }
            return parts;
        }

        public List<COTSParticleClr> GetLeftBorderedParticles()
        {
            List<COTSParticleClr> parts = new List<COTSParticleClr>();
            foreach (var p in m_listAnalysisParticles)
            {
                var segs = p.GetFeature().GetSegmentsList();
                foreach (var seg in segs)
                {
                    if (seg.GetStart() == 0)
                    {
                        parts.Add(p);
                        break;
                    }

                }
            }
            return parts;
        }

        public List<COTSParticleClr> GetRightBorderedParticles()
        {
            List<COTSParticleClr> parts = new List<COTSParticleClr>();
            foreach (var p in m_listAnalysisParticles)
            {
                var segs = p.GetFeature().GetSegmentsList();
                foreach (var seg in segs)
                {
                    if (seg.GetStart() + seg.GetLength() == this.ImgWidth)
                    {
                        parts.Add(p);
                        break;
                    }

                }
            }
            return parts;
        }

        // is empty
        public bool IsEmpty()
        {
            return m_listAllParticles.Count == 0;
        }
        void Duplicate(COTSField a_oSource)
        {

            m_nID = a_oSource.m_nID;
            m_otsPos = a_oSource.m_otsPos;


            // copy data over
            foreach (var pParticle in a_oSource.m_listAllParticles)
            {
                m_listAllParticles.Add(pParticle);
            }
        }

        public override void Serialize(bool isStoring, XmlDocument classDoc, XmlNode rootNode)
        {
            xPoint xPos = new xPoint();
            Slo slo = new Slo();
            slo.Register("OTSPosition", xPos);


            if (isStoring)
            {

                xPos.AssignValue(new System.Drawing.Point((int)m_otsPos.X, (int)m_otsPos.Y));
                slo.Serialize(true, classDoc, rootNode);
            }
            else
            {
                slo.Serialize(false, classDoc, rootNode);
                m_otsPos = xPos.value();
            }
        }
    }





}