OTS/OTSIncAMeasureApp/1-OTSMeasure/Measure/3-MeasureFlow/CSmplMeasure.cs

using System;
using System.Collections.Generic;
using System.Linq;



using OTSModelSharp.ServiceCenter;
using static OTSDataType.otsdataconst;
using OTSDataType;

using System.Drawing;
using System.Threading;
using OTSModelSharp.DTLBase;
using OTSCLRINTERFACE;
using OTSMeasureApp._0_OTSModel.OTSDataType;
using System.Windows.Forms;
using System.Data;
using System.IO;
using OTSMeasureApp._1_OTSMeasure.Measure._3_MeasureFlow;

namespace OTSModelSharp
{

    using CHoleBSEImgsList = List<CHoleBSEImg>;
 
   

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

       protected CSmplMsrResult m_pSampleRstFile;
        CHoleBSEImgsList m_listHoleBSEImg;
        
        protected ISemController m_SemHardwareMgr;
        protected IScanController m_ScanHardwareMgr;
        protected IEDSController m_EDSController;
      
        protected Queue<COTSFieldData> fieldQueue=new Queue<COTSFieldData>();
      
        protected IClassifyEngine m_classifyEngine;
       

        public CSmplMeasure( string a_strWorkingFolder, COTSSample a_pSample)
        {
            m_Sample = a_pSample;
                log = NLog.LogManager.GetCurrentClassLogger();
            var expC = m_Sample.GetMsrParams().GetXRayParam().GetAnalyExpCount();
            var imgwidth = m_Sample.GetMsrParams().GetImageScanParam().GetImageResolutionSize().cx;
            var imgheight = m_Sample.GetMsrParams().GetImageScanParam().GetImageResolutionSize().cy;


            m_strWorkingFolder = a_strWorkingFolder;
            m_pSampleRstFile = new CSmplMsrResult( a_strWorkingFolder,  a_pSample);
            m_SemHardwareMgr = SemController.GetSEMController();
            m_ScanHardwareMgr = ScanController.GetScanController();
            m_EDSController = EDSController.GetEDSController(imgwidth,imgheight,expC);
            m_listHoleBSEImg = new CHoleBSEImgsList();
            m_Sample = a_pSample;

          
        }

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


        public void SetHolePreviewSample(COTSSample a_pSample)
        {

            m_HolePreviewSample = a_pSample;
           
        }
        public COTSSample GetHolePreviewSample() { return m_HolePreviewSample; }

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

        bool SetSEMDataMrs(COTSSample sample)
        {
            var pSEMDataMsr = sample.GetSEMDataMsr();
          
            double dMag = pSEMDataMsr.GetMagnification();
            double dWorkDis = pSEMDataMsr.GetWorkingDistance();

           
            var pSEMCtrl = m_pMsrThread.GetSEMController();
   
          
            pSEMCtrl.SetMagnification(dMag);
            pSEMCtrl.SetWorkingDistance(dWorkDis);


            return true;

        }
        bool SetSEMExteralOn()
        {
            var pSEMCtrl = m_SemHardwareMgr;



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

            pSEMCtrl.SetScanExternal(true);

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


           
            log.Warn("Set SEM Exteral Off！");
            pSEMCtrlPtr.SetScanExternal(false);

            return true;
        }

        bool SetBSEParam()
        {


           
            // get scan controller
            var pScanController = m_ScanHardwareMgr;


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

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



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

            // convert dwell time to bruker dwell time (8, 16, 32)
            int nBrukerDwellTimeId;
            switch (nDwellTime)
            {
                case OTS_IMAGE_SCANSPEED_OPTIONS.low:
                    nBrukerDwellTimeId = 1;
                    break;
                case OTS_IMAGE_SCANSPEED_OPTIONS.meddium:
                    nBrukerDwellTimeId = 2;
                    break;
                case OTS_IMAGE_SCANSPEED_OPTIONS.high:
                    nBrukerDwellTimeId = 3;
                    break;
                default:
                    nBrukerDwellTimeId = 1;
                    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(COTSSample sample)
        {

            // get scan controller
            var pScanController = m_ScanHardwareMgr;


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

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


            // get dwell time 
            OTS_IMAGE_SCANSPEED_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 ImageSize");
                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(COTSSample sample, out List<System.Drawing.Point> a_allpieldcenter, out List<System.Drawing.Point> a_listUnMsrFieldCenter)
        {

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


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

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

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

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

            a_allpieldcenter = pFieldMgr.GetFieldCentrePoints();

            // ok, return TRUE
            return true;

        }
        protected bool IsAborted()
        {
           
            return m_pMsrThread.IsMeasureStopped();
        }
        protected bool IsPaused()
        {
            
            var statu = m_pMsrThread.GetMsrThreadStatus();
            if (statu.GetStatus() == OTS_MSR_THREAD_STATUS.PAUSED)
            {
                return true;
            }
            else 
            {
                return false;
            }
            
        }

        bool IsSampleOver(COTSImgScanPrm  a_pScanParam)
        {
          

            string sStopMode = a_pScanParam.GetStopMode();
            int nStopField = a_pScanParam.GetStopParamFields();

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

            CMsrResultItems pMsrResults = m_Sample.GetMsrResults();
            List<CMsrResultItem> listMsrResult = pMsrResults.GetResultItems();
            int nNumParticle = 0;
            foreach (var pResult in listMsrResult)
            {
                if (pResult.GetTypeId() > (int)OTS_PARTICLE_TYPE.NOT_IDENTIFIED)//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 NMeasArea = (int)pMsrResults.GetMeasuredArea();

            int nParticlAim = a_pScanParam.GetStopParamParticles();
            int nMeasTimeAim = a_pScanParam.GetStopParamMeasTime();
            int NMeasAreaAim = a_pScanParam.GetStopParamArea()*1000000 ;

            bool bRet = false;

            string[] str = sStopMode.Replace(" ", "").Split('+');
            for(int i=0;i< str.Length;i++)
            {
                switch (int.Parse(str[i].Split(':')[0])-1)
                {
                    case (int)OTS_MEASURE_STOP_MODE.CoverMode:
                        // completed fields number
                        if (nCompeltedField == m_Sample.GetFieldsData().Count)
                        {

                            bRet = true;
                        }
                        break;
                    case (int)OTS_MEASURE_STOP_MODE.FieldMode:
                        if (nCompeltedField >= nStopField)
                        {

                            bRet = true;
                        }
                        break;
                    case (int)OTS_MEASURE_STOP_MODE.ParticleMode:

                        if (nNumParticle >= nParticlAim)
                        {

                            bRet = true;
                        }
                        break;
                    case (int)OTS_MEASURE_STOP_MODE.TimeMode:

                        if (nUsedTime >= nMeasTimeAim)
                        {

                            bRet = true;
                        }
                        break;
                    case (int)OTS_MEASURE_STOP_MODE.AreaMode:

                        if (NMeasArea >= NMeasAreaAim)
                        {

                            bRet = true;
                        }
                        break;
                    default:
                        break;
                }
            }

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


            PointF a_SEMpt = new Point();
       
            CSEMStageData a_pCSEMStageData = m_pMsrThread.GetProjResultData().GetSEMStageData();
            int hardWareDelay = a_pCSEMStageData.GetHardWareDelay();


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

            log.Info("Begin to move SEM stage to OTScoord:" + a_poi.X + "," + a_poi.Y);

            log.Info("Begin to move SEM stage to " + a_SEMpt.X + "," + a_SEMpt.Y);
           
            // move SEM to the position (rotation 0)
            if (!pSEMController.MoveSEMToPoint(a_SEMpt.X, a_SEMpt.Y))
            {
                log.Error("MoveSEMToPoint: failed to call MoveSEMToPoint method.");
                return false;
            }
            CSampleParam pMsrParam = m_Sample.GetMsrParams();
            if (pMsrParam.SlopParam.IsUsingSlopParam)
            {
                double wd = pMsrParam.SlopParam.GetWD(a_SEMpt);
                double originWd = 0;
                pSEMController.GetWorkingDistance(ref originWd);
                if ((wd - originWd) > 2)
                {
                    log.Warn("Working Distance is invalid,outof the moving scope(2cm)  wd=" + wd.ToString("F2"));

                }
                else 
                {
                    Thread.Sleep(hardWareDelay);
                    pSEMController.SetWorkingDistance(wd);
                }

              
            }
            if (hardWareDelay > 0)
            {
                Thread.Sleep(hardWareDelay);
            }
           
            return true;
        }
        // Acquire a BSE image
        CBSEImgClr AcquireABSEImage()
        {
            // BSE image
            CBSEImgClr pBSEImage = null;

            // get scan controller
            var pScanController = m_ScanHardwareMgr;


            pBSEImage = pScanController.AcquireBSEImage();
            

            return pBSEImage;
        }

        public bool IsLowCounts(COTSParticleClr particle)
        {
            COTSXRayParam pXRayParam = m_Sample.GetMsrParams().GetXRayParam();

            if (pXRayParam.GetUsingXray() == true)
            {
                var thecount = particle.GetXray().GetTotalCount();
                var expect = pXRayParam.GetAnalyExpCount();


                if (thecount < expect)
                {

                    particle.SetType((int)OTS_PARTICLE_TYPE.LOW_COUNT);
                    particle.SetTypeColor("#000000");
                    particle.SetTypeName("LowCounts");
                    return true;
                }
            }
            return false;
        }
        public virtual void ClassifyFieldParticles(COTSFieldData curFldData)
        {
            return;
        }
      
        private class SEMStateObject
        {
            private PointF pos;
            private double workingDistance;
            private CSEMDataGnr semdata;
            private COTSSample originalSample;
            private double magnification;
            public PointF Pos { get => pos; set => pos = value; }
            public double WorkingDistance { get => workingDistance; set => workingDistance = value; }
            public CSEMDataGnr Semdata { get => semdata; set => semdata = value; }
            public double Magnification { get => magnification; set => magnification = value; }
            public COTSSample OriginalSample { get => originalSample; set => originalSample = value; }
        }
        private class AutoResetSEMControl:IDisposable
        {
            CSmplMeasure sm;
            private SEMStateObject semState=null;
            public AutoResetSEMControl(CSmplMeasure s)
            {
                sm = s;
            }

            public SEMStateObject SemState 
            { 
                get => semState; 
                set => semState = value; 
            }

            public void Dispose()
            {
                if (semState != null)
                {
                    sm.SetBSEParam();
                   
                    sm.m_SemHardwareMgr.SetMagnification(semState.Magnification);
                    Thread.Sleep(100);
                    sm.MoveSEMToPoint(semState.Pos);
                    Thread.Sleep(100);
                    sm.m_SemHardwareMgr.SetWorkingDistance(semState.WorkingDistance);
                   

                }
                sm.SetSEMExteralOff();
            }
        }
        private bool GetSEMDataGnrFromHw(ref CSEMDataGnr SemDataGnr)
        {
            double kv = 0, brightness = 0, contrast = 0;
          
                var hw = SemController.GetSEMController();
                hw.GetSemHighTension(ref kv);
                hw.GetSemBrightness(ref brightness);
                hw.GetSemContrast(ref contrast);
           

            SemDataGnr.SetValue(kv, brightness, contrast);
            return true;
        }
        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(m_Sample);
                MsgSmpStart.InitSampleStartMsg();

                m_pMsrThread.SendMessageToMeasureGUI(MsgSmpStart);

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

              
                //-----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())
                {// 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;
                }

                //------
                var FldDatas = m_Sample.GetFieldsData();

              
                if (m_EDSController.GetEDSType()==EDSTYPE.BRUKER && m_Sample.GetMsrParams().GetXRayParam().GetUseFilter())
                {
                    List<string> KeyNameList = new List<string>();
                    string DBAddress = Application.StartupPath + "\\Config\\SysData\\" + m_Sample.GetMsrParams().GetSTDName() + ".db";
                    SQLiteHelper sQLiteHelper = new SQLiteHelper(DBAddress);//
                    KeyNameList = sQLiteHelper.GetDBKeyElementList("ClassifySTD", "KeyElementList");
                    m_EDSController.SetFilterKeyEleNames( KeyNameList);//will decide if do the quantification according to this keyelelist.
                }
               
                for (int i = 0; i < FldDatas.Count; ++i)
                {// check and break if stop button is clicked
                   
                    var curFld = FldDatas[i];
                    if (curFld.GetIsMeasureComplete())
                    {
                        continue;
                    }
                    if (IsPaused())
                    {// measure stopped			
                        pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.PAUSED);
                        // 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);
                        }

                        SetSEMExteralOff();
                        // update thread measure status class, let the main thread know that this sample measurement stopped
                        ST_MSTMsg MsgSmpStop = new ST_MSTMsg(m_Sample);

                        MsgSmpStop.InitSamplePausedMsg();
                       
                        m_pMsrThread.SendMessageToMeasureGUI(MsgSmpStop);
                        while (IsPaused())
                        {
                            Thread.Sleep(300);
                        
                        }
                       
                    }
                    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);
                        }
                        break;
                    }
                   
                    // check if sample measurement completes
                    COTSImgScanPrm pScanParam = m_Sample.GetMsrParams().GetImageScanParam();
                 
                    if (IsSampleOver(pScanParam))
                    {
                        pStatus.SetStatus(OTS_MSR_SAMPLE_STATUS.SUCCESSED);
                        pStatus.ComputeTime(OTS_MSR_TIME_TYPE.COMPLT);
                        break;
                    }

                    // get a field center 
                    System.Drawing.PointF poiFieldCentre = curFld.GetOTSPosition();

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

                    ST_MSTMsg MsgFieldStart = new ST_MSTMsg(m_Sample,curFld);

                    MsgFieldStart.InitFieldStartMsg();

                    m_pMsrThread.SendMessageToMeasureGUI(MsgFieldStart);
                    int fldNo = curFld.GetId();
                    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;
                    }
                    curFld.SetBSEImage(pBSEImg);


                    //BSEData
                    ST_MSTMsg MsgFieldBSE = new ST_MSTMsg(m_Sample,curFld);
                    MsgFieldBSE.InitFieldBSEImageMsg();

                    m_pMsrThread.SendMessageToMeasureGUI(MsgFieldBSE);
                  

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

                    // image process

                    FieldImageProcess(curFld);

                    COTSXRayParam pXRayParam = m_Sample.GetMsrParams().GetXRayParam();

                    if (pXRayParam.GetUsingXray() == true)
                    {

                       CollectParticlesXrayData(curFld);


                    }

                    m_Sample.GetMsrStatus().SetStatus(OTS_MSR_SAMPLE_STATUS.SUCCESSED);


                    curFld.SetIsMeasureComplete(true);

                    log.Info("Begin to classify particles! particle num:" + curFld.GetListAnalysisParticles().Count);
                    ClassifyFieldParticles(curFld);
                    //start db save
                    StartSaveFileThread(ref curFld);

                    SendFieldParticlesInfoToGUI(curFld, m_Sample.GetMsrStatus());
                }


                while (bSaveThreadWorking)//wait untill all the field data has been saved.
                {
                    Thread.Sleep(1000);
                    log.Warn("db saving!");
                }

                TheLastWorkOfSampleMeasure();
            }
    }
        public void TheLastWorkOfSampleMeasure()
        {
            COTSSample theSample = m_Sample;
            var pStatus = theSample.GetMsrStatus();
           

            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(m_Sample);
            MsgSmplEnd.InitSampleCompleteMsg();
          
            m_pMsrThread.SendMessageToMeasureGUI(MsgSmplEnd);

            string userdB = m_Sample.GetMsrParams().GetSTDName();
            if(userdB.ToLower() != "nostddb" && userdB.ToLower() != "nostddb.db")
            {
                try
                {
                    string userdBpath= Application.StartupPath + "\\Config\\SysData\\" + m_Sample.GetMsrParams().GetSTDName() + ".db";
                    File.Copy(userdBpath, m_pSampleRstFile.GetFieldFileSubFolderStr().Remove(m_pSampleRstFile.GetFieldFileSubFolderStr().IndexOf("FIELD_FILES")) + m_Sample.GetMsrParams().GetSTDName() + ".db", true);
                }
                catch(Exception ex)
                {
                    MessageBox.Show("userdB copy failed:" + ex.ToString());
                }
            }
        }

        public bool DoMEasureForReMeasure()
        {
            return true;
        }

     
        public virtual void FieldImageProcess(COTSFieldData curFldData)
        {

            PointF fldCenter = curFldData.OTSPos;
           
           
            CSEMStageData a_pCSEMStageData = m_pMsrThread.GetProjResultData().GetSEMStageData();
            PointF semPos = new Point();
            a_pCSEMStageData.ConvertOTSToSEMCoord(fldCenter, ref semPos);

            curFldData.SetSemPos(semPos);

            //first step:remove background of the bse image and compound all the finded particles.

            log.Info("Begin to process image and get all particles!");
            GetOriginalParticles(ref curFldData);

            // second step :filter the finded particles.
            log.Info("Begin to filter particles!");

            FilterParticles(ref curFldData);

            CalculateParticleAbsolutPos(ref curFldData);

            log.Info("Begin to Calculate the image property of every particle!");
            var analysisparts = curFldData.GetListAnalysisParticles();
            curFldData.CalParticleImageProp(analysisparts);//calculate particle image property such as feret diameter, DMAX etc.

          
            return ;

        }

        private void FilterParticles(ref COTSFieldData curFldData)
        {
          
            var listXray = curFldData.GetAllParticles().OrderByDescending(x => x.GetActualArea()).ToList();
            var listXray1 = new List<COTSParticleClr>();
            var pXRayParam =m_Sample.GetMsrParams().GetXRayParam();
            if (listXray.Count > pXRayParam.GetXrayLimit())
            {
                for (var i = 0; i < pXRayParam.GetXrayLimit(); i++)
                {

                    listXray1.Add(listXray[i]);
                }

            }
            else
            {
                listXray1 = listXray;
            }

            curFldData.SetListAnalysisParticles(listXray1);

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


        }

        public void GetOriginalParticles(ref COTSFieldData curFldData)
        {
        
            // get image process parameter
            CSampleParam pMsrParam = m_Sample.GetMsrParams();
            COTSImageProcParam pImgProcessParam = pMsrParam.GetImageProcessParam();
            var specialPartsparam = pMsrParam.GetSpecialGrayRangeParam();
            var pixelsize = m_Sample.CalculatePixelSize();
            if (specialPartsparam != null && specialPartsparam.GetIsToRun())
            {
                List<CSpecialGrayRange> ranges = pMsrParam.GetSpecialGrayRangeParam().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());
                    curFldData.GetPartsBySpecialGray(range, diaRange, pixelsize, grayRange.ifCollectXray);
                }
            }
            var ifCollectxray = pMsrParam.GetXRayParam().GetUsingXray();
            // remove BES image background
            curFldData.RemoveImgBGAndGetParticles(pImgProcessParam, pixelsize, ifCollectxray);


            // check if this is an empty image
            if (curFldData.NoParticle())
            { // empty fields
                log.Info("ImageProcess: empty field.");
                return;
            }

          
            double dPixelSize = m_Sample.CalculatePixelSize();
            curFldData.InitParticles(pImgProcessParam, dPixelSize);
            return;
        }
       
        public virtual void CollectParticlesXrayData(COTSFieldData curFldData)
        {
          
            var allParts = curFldData.GetListXrayParticles();
          
            var smallparts = new List<COTSParticleClr>();
            var bigparts = new List<COTSParticleClr>();

            double quantifyThreshold = m_Sample.GetMsrParams().GetXRayParam().GetFeatureModeMinSize();
            foreach (var part in allParts)
            {
                double equalCircleDiameter = Math.Sqrt(part.GetActualArea() / 3.14159) * 2f;
                if (equalCircleDiameter < quantifyThreshold)
                {
                    smallparts.Add(part);
                }
                else
                {
                    bigparts.Add(part);
                }
            }

            log.Info("SmallQuantifyParts (<" + quantifyThreshold.ToString("f2") + "): " + smallparts.Count);
            log.Info("BigQuantifyParts (>=" + quantifyThreshold.ToString("f2") + "): " + bigparts.Count);

            curFldData.CreateXrayList(smallparts);
            curFldData.CreateXrayList(bigparts);

            // get x-ray parameters
            COTSXRayParam pXRayParam = m_Sample.GetMsrParams().GetXRayParam();
            var workmode = pXRayParam.GetScanMode();
           
            if (workmode == OTS_X_RAY_SCAN_MODE.PointMode)
            {

                uint nXRayAQTime;

                if (bigparts.Count > 0)
                {
                    nXRayAQTime = (uint)pXRayParam.GetMidAnalyAQTime();
                    log.Info("Begin to collect xraydata:" + bigparts.Count +"(" +nXRayAQTime.ToString()+") on " + workmode.ToString());
                    
                    m_EDSController.GetXRayByParts(bigparts, nXRayAQTime, true);

                }
                if (smallparts.Count > 0)
                {
                    Thread.Sleep(500);//add delay here,or else the eds system will halt.
                    nXRayAQTime = (uint)pXRayParam.GetSmallPartXrayTime();

                    log.Info("Begin to collect xraydata:" + smallparts.Count + "(" + nXRayAQTime.ToString() + ") on " + workmode.ToString());
                   
                    m_EDSController.GetXRayByParts(smallparts, nXRayAQTime, true);

                }

            }
            else if (workmode == OTS_X_RAY_SCAN_MODE.FeatureMode)
            {
              
                uint nXRayAQTime;
               
                if (bigparts.Count > 0)
                {
                        log.Info("Begin to collect xraydata:" + bigparts.Count + " on " + OTS_X_RAY_SCAN_MODE.FeatureMode.ToString());
                        nXRayAQTime = (uint)pXRayParam.GetMidAnalyAQTime();
                        m_EDSController.GetXRayByFeatures(bigparts, nXRayAQTime, true);

                }
                if (smallparts.Count > 0)
                {
                    Thread.Sleep(500);
                    log.Info("Begin to collect xraydata:" + smallparts.Count + " on " + OTS_X_RAY_SCAN_MODE.PointMode.ToString());
                    nXRayAQTime = (uint)pXRayParam.GetSmallPartXrayTime();
                    m_EDSController.GetXRayByParts(smallparts, nXRayAQTime, true);

                }


            }
           
            return;
        }

        public virtual void QuantifyParticlesXrayData(COTSFieldData curFldData)
        {
            var parts = curFldData.GetListXrayParticles();
            foreach (var p in parts)
            {
                m_EDSController.QuantifyXrayByPart(p);
            }
           
        
        }

        public void DoHolePreview()
        {
            using (AutoResetSEMControl autoReset = new AutoResetSEMControl(this))
            {
                //----------memorize the state of sem
                var semstate = new SEMStateObject();
             
                 double dMagnification = m_Sample.GetSEMDataMsr().GetMagnification();
               double wd = m_Sample.GetSEMDataMsr().GetWorkingDistance();
                ISemController sem = m_SemHardwareMgr;
                double posX=0, posY=0,posR=0;
                sem.GetSemPositionXY(ref posX, ref posY, ref posR);

                CSEMStageData a_pCSEMStageData = m_pMsrThread.GetProjResultData().GetSEMStageData();

                Point pos = new Point((int)posX, (int)posY);
                PointF otsPos = new Point(0, 0);

                if (!a_pCSEMStageData.ConvertSEMToOTSCoord(pos, ref otsPos)) 
                {
                    return;
                }
                semstate.Pos = otsPos;
                semstate.Magnification = dMagnification;
                semstate.WorkingDistance = wd;

                autoReset.SemState = semstate;


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

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



                // get SEM controller to set magnification and working distance
                if (!SetSEMDataMrs(m_HolePreviewSample))
                {
                    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;
                }

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

                    return;
                }

            


                // calculate field centers
                List<System.Drawing.Point> listFieldCenter;
                List<System.Drawing.Point> alllistFieldCenter ;
              
                if (!CalculateUnMeasuredFieldsCenters(m_HolePreviewSample, 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;
               
 

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

             


                    // 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(m_HolePreviewSample);

                    MsgFieldBSE.InitHolePreBSEDataMsg(pBSEIamge,poiFieldCentre);
                  


                    m_pMsrThread.SendHolePreviewMessageToMeasureGUI(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
                    Rectangle oImageRect = (Rectangle)pBSEIamge.GetImageRect();
                    CHoleBSEImg pHoleBSEImg =new CHoleBSEImg(oImageRect,poiFieldCentre);
                 
                    pHoleBSEImg.SetImageData( pBSEIamge.GetImageDataPtr(),oImageRect.Width,oImageRect.Height);

                    m_listHoleBSEImg.Add(pHoleBSEImg);

                }

                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(m_HolePreviewSample);

                MsgSmplEnd.InitHolePreSampleEndMsg();
               
              
                m_pMsrThread.SendHolePreviewMessageToMeasureGUI(MsgSmplEnd);

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

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

            // cumulate field data info
        
            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);
            }
            m_Sample.SetMsrResults(pMsrResults);
            // ok, return TRUE
            return true;
        }

      


       
        public bool SaveFieldData(COTSFieldData fldData, string filedFileFoler)
        {
           
            string strFieldFileFolder = filedFileFoler;

            CBSEImageFileMgr pBSEImgFileMgr = new CBSEImageFileMgr();
            pBSEImgFileMgr.SetBSEImg(fldData.GetBSEImage());
            int nId = fldData.GetId();
            string sFieldId;
            sFieldId = nId.ToString();


            string strBSEFilePathname = strFieldFileFolder + "\\" + m_pSampleRstFile.SMPL_MSR_RESULT_FIELDS_BSE + sFieldId + pBSEImgFileMgr.BMP_IMG_FILE_EXT;
            if (!pBSEImgFileMgr.SaveIntoBitmap(strBSEFilePathname))
            {
                log.Error("SaveFieldFiles: save BSE file failed.");
                return false;
            }

            // IncA Data list

            CIncAFileMgr pDBFileMgr = m_pSampleRstFile.DBFileMgr;




            pDBFileMgr.SaveStatusDataToDB();
            var fldDB = pDBFileMgr.GetFieldDB();

            log.Warn("Start saving particle data.");

            var fldcmd = fldDB.GetSavingAFieldcmdObj(fldData.GetId(), fldData.GetOTSPosition(), fldData.GetSemPos());

            List<KeyValuePair<string, System.Data.SQLite.SQLiteParameter[]>> fldcmds = new List<KeyValuePair<string, System.Data.SQLite.SQLiteParameter[]>>();
            fldcmds.Add(fldcmd);
            pDBFileMgr.ExecuteNonQueryBatch(ref fldcmds);
            //remomove the invalid particles




            var cmds = pDBFileMgr.GetSavingParticleDataToDBCmds(fldData.GetListAnalysisParticles(), fldData.GetOTSPosition());

            pDBFileMgr.ExecuteNonQueryBatch(ref cmds);


            CPosXrayDBMgr PosXrayDBMgr = pDBFileMgr.GetPosXrayDBMgr();
            var listAnalysisPosXray = new List<CPosXrayClr>();
            foreach (var p in fldData.GetListXrayParticles())
            {
                listAnalysisPosXray.Add(p.GetXray());
            }


            var cmds1 = PosXrayDBMgr.GetSavingXrayCmds(listAnalysisPosXray, true);

            pDBFileMgr.ExecuteNonQueryBatch(ref cmds1);



            return true;
        }
        protected void SaveFieldMgrData()
        {
            while (bSaveThreadWorking)
            {
                while (fieldQueue.Count() > 0)
                {
                    COTSFieldData f = fieldQueue.Dequeue();
              
                    //save to disk first ,then pop . if the size is 0,then we know all the saving work is done.
                    log.Info("Begin to save particles data! particle num:" + f.GetListAnalysisParticles().Count);
                    SaveFieldData(f, m_pSampleRstFile.GetFieldFileSubFolderStr());

                  
                }
                if (fieldQueue.Count() == 0)
                {
                    bSaveThreadWorking = false; //must set this flag,so the main thread can know this thread has exited.
                    log.Warn("finished batch saving");
                    return;
                }
            }
            return;
        }
        private void SendFieldParticlesInfoToGUI(COTSFieldData curFld,CMsrSampleStatus pStatus)
        {
            double measuredArea = 0; // this area should be the field area
            var a_pBSEImg = curFld.GetBSEImage();

            double dPixelSize = curFld.GetPixelSize();


            measuredArea = a_pBSEImg.GetHeight() * a_pBSEImg.GetWidth() * dPixelSize * dPixelSize; //Get measured area

            CumulateFieldData(curFld.GetListAnalysisParticles(), measuredArea);

            log.Info("Send field data to screen!");

            pStatus.AddCompletedFieldCenter(curFld.OTSPos);
            //Field Data
            // record end time
            pStatus.ComputeTime(OTS_MSR_TIME_TYPE.STOPPED);
            ST_MSTMsg MsgFieldEnd = new ST_MSTMsg(m_Sample,curFld);
            MsgFieldEnd.InitFieldDataMsg();
           

            m_pMsrThread.SendMessageToMeasureGUI(MsgFieldEnd);


        }

        protected void StartSaveFileThread(ref COTSFieldData a_pFieldMgr)
        {


            fieldQueue.Enqueue(a_pFieldMgr);


            if (fieldQueue.Count() > 0) //if there's data in the queue and the previous thread has finished then start a new thread.
            {
                if (bSaveThreadWorking == false)
                {
                    bSaveThreadWorking = true;

                    m_thread_ptr = new System.Threading.Thread(this.SaveFieldMgrData);//m_thread_ptr = shared_ptr<thread>(new thread(&CSmplMeasureInc::SaveFieldMgrData, this));
                    m_thread_ptr.IsBackground = true;
                    m_thread_ptr.Start();
                }
            }
        }
        public void ParticleSpecialTreatment(ref COTSFieldData fld)
        {
            //we adopt such a strategy here:if some particles satisfy the predefined condition then we go through the second collecting with max EDS time,so that we got a more acurate result.
            Dictionary<COTSParticleClr, int> mapPartXray = new Dictionary<COTSParticleClr, int>();   
            double edsTime = 0; //to store the EDSTime returned from the engine.
            var bigparts = fld.GetListXrayParticles();
            var m_ClassifyEngine = new CClassifyEngine();
            for (int i = 0; i < bigparts.Count(); i++)
            {
                var engine = m_ClassifyEngine.GetExpressionClassifyEngine(m_Sample.GetMsrParams().GetSTDName());
                var p = bigparts[i];

                // there will be very less particle satisfied the condition ,so we use only one MaxEDS time,though we set MaxEDSTime for every rule separately .Here we store the last one.
                //if the particle satisfied the MaxEDS condition then we go through the second colleting.Here we record the particle and the EDSTime and the corresponding xray position.
                edsTime = engine.IfNeedMaxEDS(p);
                if (edsTime > 0)
                {
                    mapPartXray[p] = i;
                }
            }
            List<COTSParticleClr> partsMax = new List<COTSParticleClr>();
            if (mapPartXray.Count() > 0)
            {
                foreach (var p in mapPartXray)
                {
                    partsMax.Add(p.Key);
                }
                List<CPosXrayClr> maxEDSXrays = new List<CPosXrayClr>();
                m_EDSController.GetXRayByFeatures(partsMax, edsTime, true);



            }
        }
        public void CalculateParticleAbsolutPos(ref COTSFieldData curFldData)
        {
            double dPixelSize = m_Sample.CalculatePixelSize();
            CSEMStageData pCSEMStageData = m_pMsrThread.GetProjResultData().GetSEMStageData();
            foreach (var p in curFldData.GetListAnalysisParticles())
            {

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

        }

    }
}