OTS/OTSIncAMeasureApp/0-OTSModel/Measure/3-MeasureFlow/CSmplMeasure.cs

using System;
using System.Collections.Generic;
using System.Linq;
using System.Text;
using System.Threading.Tasks;


using OTSModelSharp.ServiceInterface;
using static OTSDataType.otsdataconst;
using OTSDataType;
using System.Diagnostics;
using System.Drawing;
using System.Threading;
using OTSModelSharp.DTLBase;
using OTSCLRINTERFACE;

namespace OTSModelSharp
{

    using CHoleBSEImgsList = List<CHoleBSEImg>;


    class CSmplMeasure
    {
        protected static NLog.Logger log ;
        protected bool bSaveThreadWorking;
        protected System.Threading.Thread m_thread_ptr;
   
        protected COTSSample m_Sample;
        protected CMsrThread m_pMsrThread;
        string m_strWorkingFolder;

       protected CSmplMsrResult m_pSampleRstFile;
        CHoleBSEImgsList m_listHoleBSEImg;
        //CFunExportClass loger;
        protected SemController m_SemHardwareMgr;
        protected ScanController m_ScanHardwareMgr;
        protected EDSController m_EDSHardwareMgr;
      
        protected Queue<COTSFieldData> fieldQueue=new Queue<COTSFieldData>();
        protected COTSFieldData curFldData;
        protected IClassifyEngine m_classifyEngine;
        public CSmplMeasure()
        {
          
                log = NLog.LogManager.GetCurrentClassLogger();

           
            m_pSampleRstFile = new CSmplMsrResult();
            m_SemHardwareMgr = new SemController();
            m_ScanHardwareMgr = new ScanController();
            m_EDSHardwareMgr = new EDSController();

            m_listHoleBSEImg = new CHoleBSEImgsList();
        }

        public CSmplMeasure( string a_strWorkingFolder, COTSSample a_pSample)
        {
          
                log = NLog.LogManager.GetCurrentClassLogger();

          
            m_strWorkingFolder = a_strWorkingFolder;
            m_pSampleRstFile = new CSmplMsrResult( a_strWorkingFolder,  a_pSample);// new CSmplMsrResultFile(m_strWorkingFolder,a_pSample);
            m_SemHardwareMgr = new SemController();
            m_ScanHardwareMgr = new ScanController();
            m_EDSHardwareMgr = new EDSController();
            m_listHoleBSEImg = new CHoleBSEImgsList();
            m_Sample = a_pSample;
            
        }

       public void SetSample(COTSSample a_pSample)
        {
            
            m_Sample = a_pSample;
            m_pSampleRstFile.SetSample(a_pSample);
        }


        public void SetMsrThread(CMsrThread mt)
        {
            m_pMsrThread = mt;
           
           
        }

        bool SetSEMDataMrs()
        {
            var pSEMDataMsr = m_Sample.GetSEMDataMsr();
            //ASSERT(pSEMDataMsr);
            double dMag = pSEMDataMsr.GetMagnification();
            double dWorkDis = pSEMDataMsr.GetWorkingDistance();

            //CSemBasePtr pSEMCtrlPtr = GetSEMControl();
            var pSEMCtrl = m_pMsrThread.GetSEMController();
            // get SEM controller
            if (!pSEMCtrl.IsConnected())
            {
                if (!pSEMCtrl.Connect())
                {
                    log.Error("SetSEMDataMrs: can't connect SEM.");
                    return false;
                }
            }
            log.Info("set magnification:" + dMag.ToString());
            log.Info("set Working Distance:" + dWorkDis.ToString());
            pSEMCtrl.SetMagnification(dMag);
            pSEMCtrl.SetWorkingDistance(dWorkDis);


            return true;

        }
        bool SetSEMExteralOn()
        {
            var pSEMCtrl = m_SemHardwareMgr;


            // get SEM controller
            if (!pSEMCtrl.IsConnected())
            {
                if (!pSEMCtrl.Connect())
                {
                    log.Error("SetSEMExteralOn: can't connect SEM.");
                    return false;
                }
            }

            log.Warn("Set Scan Exteral on!");

            pSEMCtrl.SetScanExternal(true);

            return true;
        }
        // set SEM external off
        bool SetSEMExteralOff()
        {
            var pSEMCtrlPtr = m_SemHardwareMgr;


            // get SEM controller
            if (!pSEMCtrlPtr.IsConnected())
            {
                if (!pSEMCtrlPtr.Connect())
                {
                    log.Error("SetSEMExteralOff: can't connect SEM.");
                    return false;
                }
            }
            log.Warn("Set SEM Exteral Off！");
            pSEMCtrlPtr.SetScanExternal(false);

            return true;
        }

        bool SetBSEParam()
        {


            // get SEM controller 
            var pSEMController = m_SemHardwareMgr;

            // get scan controller
            var pScanController = m_ScanHardwareMgr;


            // scan parameters
            var pMsrParam = m_Sample.GetMsrParams();
            var pImgScanParam = pMsrParam.GetImageScanParam();

            // get image size
            var nImageSizeId = pImgScanParam.GetImagePixelSize();
            int nResulotionId = RESOLUTION_ID_FIRST_TIE + (int)nImageSizeId;
            Size sizePixelImage = RESOLUTION_VALUE[nResulotionId];


            // get SEM controller
            if (!pSEMController.IsConnected())
            {
                if (!pSEMController.Connect())
                {
                    log.Error("SetBSEParam: can't connect SEM.");
                    return false;
                }
            }

            // get dwell time 
            OTS_THREE_TIES_OPTIONS nDwellTime = pImgScanParam.GetScanImageSpeed();

            // convert dwell time to bruker dwell time (8, 16, 32)
            int nBrukerDwellTimeId=3;
            switch (nDwellTime)
            {
                case OTS_THREE_TIES_OPTIONS.low:
                    nBrukerDwellTimeId = 3;
                    break;
                case OTS_THREE_TIES_OPTIONS.meddium:
                    nBrukerDwellTimeId = 4;
                    break;
                case OTS_THREE_TIES_OPTIONS.high:
                    nBrukerDwellTimeId = 5;
                    break;
                default:
                    nBrukerDwellTimeId = 3;
                    break;

            }

            long nBrukerDwellTime = OTSDataType.otsdataconst.DWELLTIME_BRUKER_VALUES[nBrukerDwellTimeId];


            if (!pScanController.Init())
            {
                log.Error("SetBSEParam: failed to get scan control.");
               
                return false;
            }

            // set dwell time
            if (!pScanController.SetDwellTime(nBrukerDwellTime))
            {
                log.Error("SetBSEParam: failed to set dwell time (%d) for bruker system.", nBrukerDwellTime);
                return false;
            }

            // set image size
            if (!pScanController.SetImageSize(sizePixelImage.Width,sizePixelImage.Height))
            {
                // failed to set dwell time
                log.Error("SetBSEParam: failed to set dwell time (%d).", sizePixelImage.Height);
                return false;
            }

            return true;
        }
        bool SetHoleBSEParam()
        {


            // get SEM controller 
            var pSEMController = m_SemHardwareMgr;

            // get scan controller
            var pScanController = m_ScanHardwareMgr;


            // scan parameters
            var pMsrParam = m_Sample.GetMsrParams();
            var pImgScanParam = pMsrParam.GetImageScanParam();

            // get image size
            var nImageSizeId = pImgScanParam.GetImagePixelSize();
            int nResulotionId = RESOLUTION_ID_FIRST_TIE + (int)nImageSizeId;
            Size sizePixelImage = RESOLUTION_VALUE[nResulotionId];



            // get SEM controller
            if (!pSEMController.IsConnected())
            {
                if (!pSEMController.Connect())
                {
                    log.Error("SetBSEParam: can't connect SEM.");
                    return false;
                }
            }

            // get dwell time 
            OTS_THREE_TIES_OPTIONS nDwellTime = pImgScanParam.GetScanImageSpeed();

            // convert dwell time to bruker dwell time (6, 16, 32)
            long nBrukerDwellTime = DWELLTIME_BRUKER_VALUES[2];// choose the third option, so the dwell time will be 4 . there's no need to change here. it shoud be a const.


            if (!pScanController.Init())
            {
                log.Error("SetBSEParam: failed to get scan control.");

                return false;
            }

            // set dwell time
            if (!pScanController.SetDwellTime(nBrukerDwellTime))
            {
                log.Error("SetBSEParam: failed to set dwell time (%d) for bruker system.", nBrukerDwellTime);
                return false;
            }

            // set image size
            if (!pScanController.SetImageSize(sizePixelImage.Width/2, sizePixelImage.Height/2))
            {
                // failed to set dwell time
                log.Error("SetBSEParam: failed to set dwell time (%d).", sizePixelImage.Height);
                return false;
            }

            return true;
        }
        
        public  void SetWorkingFolder(String a_strWorkingFolder)
        {
            // add "\\" at the string end if it is not "\\"
            if (a_strWorkingFolder.PadRight(1)!="\\")
            {
                a_strWorkingFolder += "\\";
            }

            m_strWorkingFolder = a_strWorkingFolder + m_Sample.GetName() + "\\";
        }
        bool CalculateUnMeasuredFieldsCenters(out List<System.Drawing.Point> a_allpieldcenter,out List<System.Drawing.Point> a_listFieldCenter)
        {       

            // sample measure parameters
            CSampleParam pMsrParam = m_Sample.GetMsrParams();
            COTSImgScanPrm  poImageScanParam = pMsrParam.GetImageScanParam();
            CSEMDataMsr poSEMDataMsr = m_Sample.GetSEMDataMsr();
            CMsrSampleStatus pStatus = m_Sample.GetMsrStatus();

            // measured field centers list
            List<System.Drawing.Point> listCompletedCenter = pStatus.GetCompletedFieldsCenter();

            // field centers list manager
            CFieldPositionMgr pFieldMgr = new CFieldPositionMgr();

            // init field centers list manager
            if (!pFieldMgr.Init(m_Sample.GetMsrArea(), poImageScanParam, poSEMDataMsr, listCompletedCenter))
            {
                log.Error("CalculateFieldsCenters: failed to init field centres list manager.");
                a_listFieldCenter = new List<System.Drawing.Point>();
                a_allpieldcenter = new List<Point>();
                return false;
            }

            // get field centers list
            a_listFieldCenter = pFieldMgr.GetUnmeasuredFieldCentrePoints();// GetFieldCentrePoints();

            a_allpieldcenter = pFieldMgr.GetFieldCentrePoints();

            // ok, return TRUE
            return true;

        }
        protected bool IsAborted()
        {
            //Debug.Assert(m_pMsrThread == null);
            return m_pMsrThread.IsMeasureStopped();
        }

        bool IsSampleOver(COTSImgScanPrm  a_pScanParam, int a_nTotalFields)
        {
          

            int nStopMode = (int)a_pScanParam.GetStopMode();
            int nStopField = a_pScanParam.GetStopParamFields();

            // completed fields number
            CMsrSampleStatus pMsrSampleStatus = m_Sample.GetMsrStatus();
            int nCompeltedField = pMsrSampleStatus.GetCompletedFields();

            CMsrDisplayResults pMsrResults = m_Sample.GetMsrResults();
            List<CMsrResultItem> listMsrResult = pMsrResults.GetResultItems();
            int nNumParticle = 0;
            foreach (var pResult in listMsrResult)
            {
                if (pResult.GetTypeId() > (int)OTS_PARTCLE_TYPE.NO_ANALYSIS_X_RAY)//summarize the number of the identified particle in this condition
                {
                    nNumParticle += (int)pResult.GetNumber();
                }
            }

            TimeSpan timeSpan = pMsrSampleStatus.GetUsedTime();
            int nDay = timeSpan.Days;
            int nHour = timeSpan.Hours;
            int nMin = timeSpan.Minutes;
            int nSec = timeSpan.Seconds;
            int nUsedTime = nSec + nMin * 60 + nHour * 3600 + nDay * 86400;

            int nParticlAim = a_pScanParam.GetStopParamParticles();
            int nMeasTimeAim = a_pScanParam.GetStopParamMeasTime();

            bool bRet = true;
            switch (nStopMode)
            {
                case (int)OTS_MEASURE_STOP_MODE.CoverMode:
                    // completed fields number
                    if (nCompeltedField < a_nTotalFields)
                    {
                 
                        bRet = false;
                    }
                    break;
                case (int)OTS_MEASURE_STOP_MODE.FieldMode:
                    if (nCompeltedField < nStopField)
                    {
                     
                        bRet = false;
                    }
                    break;
                case (int)OTS_MEASURE_STOP_MODE.ParticleMode:

                    if (nNumParticle < nParticlAim)
                    {
                    
                        bRet = false;
                    }
                    break;
                case (int)OTS_MEASURE_STOP_MODE.TimeMode:

                    if (nUsedTime < nMeasTimeAim)
                    {
                      
                        bRet = false;
                    }
                    break;
                default:
                    break;
            }

            return bRet;
        }
        // move SEM to the point
        bool MoveSEMToPoint(System.Drawing.Point a_poi)
        {
            // get SEM controller 
            var pSEMController = m_SemHardwareMgr;
          


            Point a_SEMpt = new Point();
       
            CSEMStageData a_pCSEMStageData = m_pMsrThread.GetProjResultData().GetSEMStageData();
        


            if (!a_pCSEMStageData.ConverOTSToSEMPoint(a_poi, ref a_SEMpt))
            {
                return false;
            }


            if (!pSEMController.IsConnected())
            {
                if (!pSEMController.Connect())
                {
                    log.Error("MoveSEMToPoint: can't connect SEM.");
                    return false;
                }
            }
            log.Info("Begin to move SEM stage to " + a_SEMpt.X + "," + a_SEMpt.Y);
            Thread.Sleep(100);
            // move SEM to the position (rotation 0)
            if (!pSEMController.MoveSEMToPoint(a_SEMpt, 0))
            {
                log.Error("MoveSEMToPoint: failed to call MoveSEMToPoint method.");
                return false;
            }
            return true;
        }
        // Acquire a BSE image
        CBSEImgClr AcquireABSEImage()
        {
            // BSE image
            CBSEImgClr pBSEImage = null;

            // get scan controller
            var pScanController = m_ScanHardwareMgr;


            pBSEImage = pScanController.AcquireBSEImage(0, 0, 2);
      

            return pBSEImage;
        }

        public virtual bool FieldImageProcess(Point fldCenter, CBSEImgClr imageData)
        {
            return true;

        }
        public virtual void ClassifyFieldParticles()
        {
            return;
        }
        public virtual void ClassifyMergedParticles(List<COTSParticleClr> parts)
        {
            return;
        }
        private class AutoResetSEMControl:IDisposable
        {
            CSmplMeasure sm;
            public AutoResetSEMControl(CSmplMeasure s)
            {
                sm = s;
            }

         

            public void Dispose()
            {
                sm.SetSEMExteralOff();
                //sm.ResetScan();
            }
        }
         public void DoMeasureForOneSample()
        {
            using (AutoResetSEMControl autoReset = new AutoResetSEMControl(this)) //when this method exit ,the SetSEMExternalOff and ResetScan will be called automatically.
            {
                // let the main thread to know that this sample measurement starts
                var pStatus = m_Sample.GetMsrStatus();
                pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.INPROCESS);


                // set current time to current time
                pStatus.ComputeTime(OTS_MSR_TIME_TYPE.START);

                // let main App know that the sample begin to measure
                ST_MSTMsg MsgSmpStart = new ST_MSTMsg();
                MsgSmpStart.iMsgType = ENUM_MSG_TYPE.MSAMPLESTATUS;
                MsgSmpStart.STMSampleStu.iMsrSampleStatu = OTS_MSR_SAMPLE_STATUS.INPROCESS;
                MsgSmpStart.STMSampleStu.cSampleName = m_Sample.GetName();

                m_pMsrThread.SendMessageToMeasureApp(MsgSmpStart);

                log.Info(m_Sample.GetName() + " Measurement started!");
                // get SEM controller to set magnification and working distance
                if (!SetSEMDataMrs())
                {
                    log.Error("DoMeasure: fail to set SEM data.");
                    pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.FAILED);                   
                    pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);

                    return;
                }
                // get SEM external controll on
                if (!SetSEMExteralOn())
                {
                    log.Error("DoMeasure: fail to set SEM external.");
                    pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.FAILED);                  
                    pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);

                    return;
                }
                // set the BSE scan param
                if (!SetBSEParam())
                {
                    log.Error("DoMeasure: fail to set BSE param.");
                    pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.FAILED);                  
                    pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);

                    return;
                }

             
                                                            
                var pSEMDataGnr = new CSEMDataGnr();
                log.Info("Get Kv, Brightness and Contrast!");
                m_SemHardwareMgr.GetSEMDataGnrFromHw(ref pSEMDataGnr);


                m_pSampleRstFile.SetSEMGnr(pSEMDataGnr);

                // record SEM data
                COTSMsrPrjResultData pProjMgrFile = m_pMsrThread.GetProjResultData();          


                CSEMStageData pSEMStageData = pProjMgrFile.GetSEMStageData();
               

                m_pSampleRstFile.SetSEMStageData(pSEMStageData);

                // record stage
                CStage pStage = pProjMgrFile.GetStage();
              

                m_pSampleRstFile.SetSEMStage(pStage);
         
                // calculate field centers
                List<System.Drawing.Point> umMeasuredlistFieldCenter;
                List<System.Drawing.Point> alllistFieldCenter;

                if (!CalculateUnMeasuredFieldsCenters(out alllistFieldCenter,out umMeasuredlistFieldCenter))
                {// failed to calculate field centers
                    log.Error("DoMeasure: failed to calculate field centers.");
                    pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.FAILED);
                    // record end time
                    pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);
                    return;
                }
                //-----save the static measure result file data into xml file and the dynamic data of every field will be saved into sqlite database
                log.Info("Create result file!");
                if (!m_pSampleRstFile.CreateResultFiles(alllistFieldCenter))
                {// failed to call measure result file Save method
                    log.Error("DoMeasure: failed to call measure result file Save method.");
                    pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.FAILED);
                    pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);
                    return;
                }

                //------


                int nNewFieldId = 0;
                int numOfAllFields = pStatus.GetCompletedFields() + umMeasuredlistFieldCenter.Count;//
                int completedFields = pStatus.GetCompletedFields();
                log.Info("Unmeasured fields:" + umMeasuredlistFieldCenter.Count);
                for (int i = 0; i < (int)umMeasuredlistFieldCenter.Count; ++i)
                {// check and break if stop button is clicked
                    if (IsAborted())
                    {// measure stopped			
                        pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.STOPPED);
                        // record end time
                        pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);
                        //must wait for the saving data thread  finished,or we'll get null pointer exception when we stop the measure process.			
                        while (fieldQueue.Count() > 0)
                        {
                            Thread.Sleep(100);
                        }
                        return;
                    }

                    // check if sample measurement completes
                    COTSImgScanPrm pScanParam = m_Sample.GetMsrParams().GetImageScanParam();
                    int nTotalFieldSize = (int)umMeasuredlistFieldCenter.Count;



                    if (IsSampleOver(pScanParam, numOfAllFields))
                    {
                        pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);
                        break;
                    }

                    // get a field center 
                    System.Drawing.Point poiFieldCentre = umMeasuredlistFieldCenter[i];

                    // update thread measure status class, let the main thread know that starts a new field
                  

                    ST_MSTMsg MsgFieldStart = new ST_MSTMsg();
                    MsgFieldStart.iMsgType = ENUM_MSG_TYPE.MSAMPLERESULT;
                    MsgFieldStart.STMSampleRetData.iRetDataType = MSAMPLE_RET.START_MSR_FIELD;
                    MsgFieldStart.STMSampleRetData.SMsrField.FieldPos = poiFieldCentre;
                    m_pMsrThread.SendMessageToMeasureApp(MsgFieldStart);
                    int fldNo = completedFields + i + 1;
                    log.Warn("Current field:" + fldNo.ToString());
                    


                    // move SEM to the field center
                    if (!MoveSEMToPoint(poiFieldCentre))
                    {// failed to move SEM to the position
                        log.Error("DoMeasure: failed to move SEM to the field centre point.");
                        pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.FAILED);
                        // record end time
                        pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);
                        return;
                    }
                    log.Info("Begin to Acquire BSE image!");
                    // take BSE image for the fields
                    CBSEImgClr pBSEImg = AcquireABSEImage();

                    // let the main thread to know that image process is completed
                
                    if (pBSEImg == null)
                    {
                        log.Error("ImageProcess: can't get no background image.");
                        pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.FAILED);
                        return;
                    }

                  


                    //BSEData
                    ST_MSTMsg MsgFieldBSE = new ST_MSTMsg(); 

                    MsgFieldBSE.iMsgType = ENUM_MSG_TYPE.MSAMPLERESULT;
                    MsgFieldBSE.STMSampleRetData.iRetDataType = MSAMPLE_RET.BSE_DATA;
                    MsgFieldBSE.STMSampleRetData.BSEData.pos.X = poiFieldCentre.X;
                    MsgFieldBSE.STMSampleRetData.BSEData.pos.Y = poiFieldCentre.Y;
                    MsgFieldBSE.STMSampleRetData.BSEData.iBSEDataHeight = pBSEImg.GetHeight();
                    MsgFieldBSE.STMSampleRetData.BSEData.iBSEDataWidth = pBSEImg.GetWidth();
                    byte[] pImgData = pBSEImg.GetImageDataPtr();
                    MsgFieldBSE.STMSampleRetData.BSEData.lpBSEData = pImgData;

                    m_pMsrThread.SendMessageToMeasureApp(MsgFieldBSE);
                    // get a new field id

                    log.Info("Acquire BSE image success! Processing image...");

                    // image process

                 var rst = FieldImageProcess(poiFieldCentre, pBSEImg);
                    if (rst == true)
                    {
              
                            // add the field into the field
                            m_pSampleRstFile.AddAField(curFldData);

                       
                    }


                 


                    ++nNewFieldId;

                    double measuredArea = 0; // this area should be the field area
                    var a_pBSEImg = curFldData.GetBSEImage();
                    
                    double dPixelSize = m_Sample.CalculatePixelSize();
                   
                        measuredArea = a_pBSEImg.GetHeight() * a_pBSEImg.GetWidth()* dPixelSize * dPixelSize + 0.5; //Get measured area
                    if (!CumulateFieldData(curFldData.ListAnalysisParticles, measuredArea))
                    { // failed to call SaveFieldFile method
                        log.Error("ImageProcess: call CumulateFieldData method.");
                        pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.FAILED);
                        return;
                    }
                    log.Info("Send field data to screen!");
                    // completed fields
                    pStatus.SetCompletedFields(pStatus.GetCompletedFields() + 1);

                    // completed fieldCenter
                    List<System.Drawing.Point> listCpltedCenter = pStatus.GetCompletedFieldsCenter();
                    listCpltedCenter.Add(poiFieldCentre);

                    //Field Data
                    // record end time
                    pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);
                    ST_MSTMsg MsgFieldEnd = new ST_MSTMsg();                  
                    MsgFieldEnd.iMsgType = ENUM_MSG_TYPE.MSAMPLERESULT;
                    MsgFieldEnd.STMSampleRetData.iRetDataType = MSAMPLE_RET.FIELD_DATA;
                    MsgFieldEnd.STMSampleRetData.SFieldData.iCompleteFieldCount = pStatus.GetCompletedFields();
                    MsgFieldEnd.STMSampleRetData.SFieldData.iMeasureFieldCount = numOfAllFields;
                    MsgFieldEnd.STMSampleRetData.SFieldData.iSParticleCount = (int)curFldData.ListAnalysisParticles.Count;
                    MsgFieldEnd.STMSampleRetData.SFieldData.FieldPos.X = Convert.ToInt32(poiFieldCentre.X);
                    MsgFieldEnd.STMSampleRetData.SFieldData.FieldPos.Y = Convert.ToInt32(poiFieldCentre.Y);

                    m_pMsrThread.SendMessageToMeasureApp(MsgFieldEnd);

                 
                }
                while (fieldQueue.Count > 0)//wait untill all the field data has been saved.
                {
                    Thread.Sleep(100);
                }
                //merging particles
                log.Info("Merging big particles on the field edge!");
                CImageHandler imgpro = new CImageHandler();
                int scanfldsize = m_Sample.GetSEMDataMsr().GetScanFieldSize();
                List<COTSParticleClr> mergedParticles = new List<COTSParticleClr>();
                imgpro.MergeBigBoundaryParticles(m_pSampleRstFile.GetFieldData(), m_Sample.CalculatePixelSize(), scanfldsize, m_Sample.GetResolutionSize(), ref mergedParticles);

                

                ClassifyMergedParticles(mergedParticles);
                log.Warn("begin particle data db saving...");
              
           
                SaveMergedParticles(mergedParticles);
          


                pStatus.ComputeTime(OTS_MSR_TIME_TYPE.COMPLT);

                pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.SUCCESSED);

                // let main thread to know that this sample measurement completes
                ST_MSTMsg MsgSmplEnd = new ST_MSTMsg();
                MsgSmplEnd.iMsgType = ENUM_MSG_TYPE.MSAMPLESTATUS;
                MsgSmplEnd.STMSampleStu.iMsrSampleStatu = OTS_MSR_SAMPLE_STATUS.SUCCESSED;
                MsgSmplEnd.STMSampleStu.cSampleName = m_Sample.GetName();
                m_pMsrThread.SendMessageToMeasureApp(MsgSmplEnd);
            }
    }
      
        public void DoHolePreview(int a_nHoleID)
        {
            using (AutoResetSEMControl autoReset = new AutoResetSEMControl(this))
            {

                    // let the main thread to know that this sample measurement starts
                    CMsrSampleStatus pStatus = m_Sample.GetMsrStatus();
                pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.INPROCESS);

                // set current time to current time
                pStatus.ComputeTime(OTS_MSR_TIME_TYPE.START);

                // let main App know that the sample begin to measure
                ST_MSTMsg MsgSmpStart=new ST_MSTMsg();
                MsgSmpStart.iMsgType = ENUM_MSG_TYPE.MSAMPLESTATUS;
                MsgSmpStart.STMSampleStu.iMsrSampleStatu = OTS_MSR_SAMPLE_STATUS.INPROCESS;
               MsgSmpStart.STMSampleStu.cSampleName=m_Sample.GetName();


                // get SEM controller to set magnification and working distance
                if (!SetSEMDataMrs())
                {
                    log.Error("DoHolePreview: fail to set SEM data.");
                    pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.FAILED);
                    // record end time
                    pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);

                    return;
                }

                // get SEM external controll on
                if (!SetSEMExteralOn())
                {
                    log.Error("DoMeasure: fail to set SEM external.");
                    pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.FAILED);
                    // record end time
                    pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);

                    return;
                }
                // set the BSE scan param
                if (!SetHoleBSEParam())
                {
                    log.Error("DoMeasure: fail to set BSE param.");
                    pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.FAILED);
                    // record end time
                    pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);

                    return;
                }

            

                // check if measurement is aborted
                if (IsAborted())
                {// measurement aborted
                    log.Trace("DoHolePreview: measurement aborted before get SEM condition.");
                    pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.STOPPED);
                    // record end time
                    pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);

                    return;
                }

                // calculate field centers
                List<System.Drawing.Point> listFieldCenter=new List<System.Drawing.Point>();
                List<System.Drawing.Point> alllistFieldCenter = new List<System.Drawing.Point>();
                // listFieldCenter.clear();
                if (!CalculateUnMeasuredFieldsCenters(out alllistFieldCenter,out listFieldCenter))
                {// failed to calculate field centers
                    log.Error("DoHolePreview: failed to calculate field centers.");
                    pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.FAILED);
                    // record end time
                    pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);
                    return;
                }

                // go through each field
                int nNewFieldId = 0;
                for ( int i = 0; i < listFieldCenter.Count; ++i)
                {// check and break if stop button is clicked
                    if (IsAborted())
                    {// measure stopped
                        log.Trace("DoHolePreview: measure thread is stopped.");
                        pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.STOPPED);
                        // record end time
                        pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);
                        return;
                    }

                    // check if sample measurement completes
                    COTSImgScanPrm  pScanParam = m_Sample.GetMsrParams().GetImageScanParam();
                    int nTotalFieldSize = listFieldCenter.Count;
               
 

                    if (IsSampleOver(pScanParam, nTotalFieldSize))
                    {
                        pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);

                        break;
                    }

                    // get a field center 
                    System.Drawing.Point poiFieldCentre = listFieldCenter[i];

             

                    // update thread measure status class, let the main thread know that starts a new field
                    pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);

                    ST_MSTMsg MsgFieldStart=new ST_MSTMsg();
                    //memset(&MsgFieldStart, 0, sizeof(ST_MSTMsg));
                    MsgFieldStart.iMsgType = ENUM_MSG_TYPE.MSAMPLERESULT;
                    MsgFieldStart.STMSampleRetData.iRetDataType = MSAMPLE_RET.START_MSR_FIELD;
                    MsgFieldStart.STMSampleRetData.SMsrField.FieldPos = poiFieldCentre;


                    m_pMsrThread.SendMessageToMeasureApp(MsgFieldStart);

                    // move SEM to the field center
                    if (!MoveSEMToPoint(poiFieldCentre))
                    {// failed to move SEM to the position
                        log.Error("DoHolePreview: failed to move SEM to the field centre point.");
                        pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.FAILED);
                        // record end time
                        pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);

                        return;
                    }

                    // take BSE image for the fields
                    CBSEImgClr pBSEIamge = AcquireABSEImage();
                    if (pBSEIamge==null)
                    {
                        // failed to acquire a BSE image
                        log.Error("DoHolePreview: failed to acquire a BSE image.");
                        pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.FAILED);
                        // record end time
                        pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);

                        return;
                    }

                    //BSEData
                    ST_MSTMsg MsgFieldBSE=new ST_MSTMsg();
                   // memset(&MsgFieldBSE, 0, sizeof(ST_MSTMsg));
                    MsgFieldBSE.iMsgType = ENUM_MSG_TYPE.MSAMPLERESULT;
                    MsgFieldBSE.STMSampleRetData.iRetDataType = MSAMPLE_RET.BSE_DATA;
                    MsgFieldBSE.STMSampleRetData.BSEData.pos = poiFieldCentre;
                    //MsgFieldBSE.STMSampleRetData.BSEData.pos.y = poiFieldCentre.y;
                    MsgFieldBSE.STMSampleRetData.BSEData.iBSEDataHeight = pBSEIamge.GetHeight();
                    MsgFieldBSE.STMSampleRetData.BSEData.iBSEDataWidth = pBSEIamge.GetWidth();
                    byte[] pImgData = pBSEIamge.GetImageDataPtr();
                    MsgFieldBSE.STMSampleRetData.BSEData.lpBSEData = pImgData;


                    m_pMsrThread.SendMessageToMeasureApp(MsgFieldBSE);

                    if (pStatus.GetStatus() != OTS_MSR_SAMPLE_STATUS.INPROCESS)
                    {
                        // measurement failed or stopped
                        log.Error("DoHolePreview: measurement failed or stopped.");
                        pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.FAILED);
                        // record end time
                        pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);

                        return;
                    }

                    //save the result to project file
                    CHoleBSEImg pHoleBSEImg =new CHoleBSEImg();
                    pHoleBSEImg.SetHoleID(a_nHoleID);
                    pHoleBSEImg.SetPosition(poiFieldCentre);
                    Rectangle oImageRect =(Rectangle) pBSEIamge.GetImageRect();
                    int nImageSize = pBSEIamge.GetHeight() * pBSEIamge.GetWidth();
                    pHoleBSEImg.SetImageRect(oImageRect);
                    pHoleBSEImg.SetImageData( pBSEIamge.GetImageDataPtr(),oImageRect.Width,oImageRect.Height);

                    m_listHoleBSEImg.Add(pHoleBSEImg);

                    COTSMsrPrjResultData pProjMgrFile = m_pMsrThread.GetProjResultData();
                    pProjMgrFile.SetHoleBESImgList(m_listHoleBSEImg,true);

                    // prepare for the next
                    ++nNewFieldId;
                    pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);

                    ST_MSTMsg MsgFieldEnd=new ST_MSTMsg();
                   
                    MsgFieldEnd.iMsgType = ENUM_MSG_TYPE.MSAMPLERESULT;
                    MsgFieldEnd.STMSampleRetData.iRetDataType = MSAMPLE_RET.FIELD_DATA;
                    MsgFieldEnd.STMSampleRetData.SFieldData.iCompleteFieldCount = (i + 1);
                    MsgFieldEnd.STMSampleRetData.SFieldData.iMeasureFieldCount = listFieldCenter.Count;
                    MsgFieldEnd.STMSampleRetData.SFieldData.iSParticleCount = 0;
                    MsgFieldEnd.STMSampleRetData.SFieldData.FieldPos = poiFieldCentre;
                   

                    m_pMsrThread.SendMessageToMeasureApp(MsgFieldEnd);

                    //break;

                }

                pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);
                //calculate measure time
                pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.SUCCESSED);

                // let main thread to know that this sample measurement completes
                ST_MSTMsg MsgSmplEnd=new ST_MSTMsg();
                MsgSmplEnd.iMsgType = ENUM_MSG_TYPE.MTHREADSTATUS;
                MsgSmplEnd.STMThreadStu.iMsrStatu = OTS_MSR_THREAD_STATUS.COMPLETED;
              
                m_pMsrThread.SendMessageToMeasureApp(MsgSmplEnd);

            }
        }
        // Cumulate field data info
        public virtual bool CumulateFieldData( List<COTSParticleClr> listParticles, double a_nMeasuredArea)
        {

            // get measure result items of the sample
            CMsrDisplayResults pMsrResults = m_Sample.GetMsrResults();

            // cumulate field data info
            //pMsrResults.CumulateMeasureResults(listResultItems);
            pMsrResults.CumulateMeasuredArea(a_nMeasuredArea);

            // cumulate ratio
            double dRatio = 10000 * pMsrResults.GetTotalParticleArea();
            dRatio = dRatio / pMsrResults.GetMeasuredArea();
            pMsrResults.SetRatio(dRatio);


        
            // go through the particles list
            foreach (COTSParticleClr pParticle in listParticles)
            {
                // create a measure result item

                pMsrResults.CumulateMeasureResult(pParticle);
            }
            // ok, return TRUE
            return true;
        }

        // hole BSE images list
        void SetHoleBESImgList(CHoleBSEImgsList a_listHoleBSEImg, bool a_bClear/* = TRUE*/)
        {// clear the hole BSE image list if necessary 
            if (a_bClear)
            {
                m_listHoleBSEImg.Clear();
            }

            // go through the input list
            foreach (var pHoleBSEImg in a_listHoleBSEImg)
            {// add the new hole BSE image into HoleBSEImage list
                m_listHoleBSEImg.Add(pHoleBSEImg);
            }

        }


        public bool SaveMergedParticles(List<COTSParticleClr> mergedParts)
        {

            CIncAFileMgr pDBFileMgr = m_pSampleRstFile.DBFileMgr;
            var mergedpartdb = pDBFileMgr.GetMergedParticleDB();
           
 
            foreach (COTSParticleClr part in mergedParts)
            {
                mergedpartdb.SaveAParticle(part, part.GetXray(), new System.Drawing.Point(0, 0));
            }
            CPosXrayDBMgr pXrayDBMgr = pDBFileMgr.GetPosXrayDBMgr();
            CElementChemistryDB xraydb = pXrayDBMgr.GetElementChemistryDB();
            List<CPosXrayClr> ches = new List<CPosXrayClr>();
            foreach (COTSParticleClr part in mergedParts)
            {
                ches.Add(part.GetXray());
            }
            xraydb.SaveElementChemistriesList(ches);
            return true;
        }


    }
}