OTS/OTSIncAMeasureApp/0-OTSModel/Measure/2-OTSCleanliness/SmplMeasureCleanliness.cs

using System;
using System.Collections.Generic;
using System.Data.SQLite;
using System.Drawing;
using System.Linq;
using System.Text;
using System.Threading;
using System.Threading.Tasks;
using OTSCLRINTERFACE;
using OTSDataType;
using OTSModelSharp.Measure.OTSCleanliness;
using OTSModelSharp.ServiceCenter;
using OTSModelSharp.ServiceInterface;
using static OTSDataType.otsdataconst;

namespace OTSModelSharp
{
    class CSmplMeasureCleanliness : CSmplMeasure
    {

        public CSmplMeasureCleanliness(string a_strWorkingFolder, COTSSample a_pSample):base(a_strWorkingFolder,a_pSample)
        {
            SetWorkingFolder(a_strWorkingFolder);
            SetSample(a_pSample);
            m_classifyEngine = new CClassifyEngine();
        }

        // field image process
        public override bool FieldImageProcess(Point fldCenter, CBSEImgClr a_BSEImg)
        {
            int nNewFieldId;
            nNewFieldId = m_pSampleRstFile.GetIdForANewField();
            //first step:remove background of the bse image and compound all the finded particles.
            curFldData = new CFieldDataClean( a_BSEImg,m_Sample.CalculatePixelSize());
            CFieldDataClean curFldDataCln =( CFieldDataClean) curFldData;
          
            curFldData.SetId(nNewFieldId);
            curFldData.SetOTSPosition(fldCenter);
            GetOriginalParticles();
 
            // second step :filter the finded particles.
            FilterParticles((CFieldDataClean)curFldData);
            CalculateParticleAbsolutPos();
            COTSXRayParam pXRayParam = m_Sample.GetMsrParams().GetXRayParam();
            //collect xray data.
            if (pXRayParam.GetUsingXray() == true)
            {
                Thread.Sleep(100);
                CollectParticlesXrayData((CFieldDataClean)curFldData);
                Thread.Sleep(100);
            }
      



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


            ClassifyFieldParticles();

  

            // save field files
            m_Sample.GetMsrStatus() .SetStatus(OTS_MSR_SAMPLE_STATUS.SUCCESSED);

            StartSaveFileThread(curFldData);

            return true;

        }
        public void CalculateParticleAbsolutPos()
        {
            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);
                Point semPos = new Point();
                pCSEMStageData.ConverOTSToSEMPoint(fldOtsPos, ref semPos);
                p.SetAbsolutPos(semPos);
            }

        }


        // save field data
        protected void SaveFieldMgrData()
        {
            while (bSaveThreadWorking)
            {
                while (fieldQueue.Count() > 0)
                {
                    CFieldDataClean f = (CFieldDataClean) fieldQueue.Dequeue();
                    double pixelSize = m_Sample.CalculatePixelSize();

          

                    //save to disk first ,then pop . if the size is 0,then we know all the saving work is done.
                    SaveFieldFiles(f,m_pSampleRstFile.GetFieldFileSubFolderStr());


                }
                if (fieldQueue.Count() == 0)
                {
                    bSaveThreadWorking = false; //must set this flag,so the main thread can know this thread has exited.
                    return;
                }
            }
            return;
        }


        protected void StartSaveFileThread(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.Start();//m_thread_ptr->detach();
                }
            }
        }

        public void FilterParticles(CFieldDataClean fld)
        {
            // 1)remove over sized particles, too small particles and get a analysis particles list
           
            double dPixelSize = m_Sample.CalculatePixelSize();


          
           
            CSampleParam pMsrParam = m_Sample.GetMsrParams();
            COTSImageProcParam pImgProcessParam = pMsrParam.GetImageProcessParam();
            var pXRayParam = pMsrParam.GetXRayParam();
            curFldData.InitParticles(pImgProcessParam, dPixelSize);
            if (curFldData.NoAnalysisParticle())
            {
                log.Warn("There's no analysis particles!");
            }

            var listXray = curFldData.GetListAnalysisParticles().OrderByDescending(x => x.GetActualArea()).ToList();
            var listXray1 = new List<COTSParticleClr>();

            if (listXray.Count > pXRayParam.GetXrayLimit())
            {
                for (var i = 0; i < pXRayParam.GetXrayLimit(); i++)
                {

                    listXray1.Add(listXray[i]);
                }

            }
            else
            {
                listXray1 = listXray;
            }



            //2) according to the quantify threshold size value saperate the analysis particles into two group :the bigparticles and the smallparticles.

            double quantifyThreshold = m_Sample.GetMsrParams().GetXRayParam().GetFeatureModeMinSize();

            var smallparts = fld.ListSmallParticles;
            var bigparts = fld.ListBigParticles;


            foreach (var part in listXray1)
            {
                double equalCircleDiameter = Math.Sqrt(part.GetActualArea() / 3.14159) * 2f;
                if (equalCircleDiameter < quantifyThreshold)
                {
                    smallparts.Add(part);
                }
                else
                {
                    bigparts.Add(part);
                }
            }
            

            fld.ListSmallParticles = smallparts;
            fld.ListBigParticles = bigparts;
            //fld.SmallParticlePercentage=percentage;
            log.Info("SmallQuantifyParts (<" + quantifyThreshold.ToString("f2") + "): " + smallparts.Count);
            log.Info("BigQuantifyParts (>=" + quantifyThreshold.ToString("f2")+ "): " + bigparts.Count);

            return ;
        }

        public void CollectParticlesXrayData(CFieldDataClean fld)
        {
            // get x-ray parameters
            COTSXRayParam pXRayParam = m_Sample.GetMsrParams ().GetXRayParam();

            // calculate search x-ray acquire time
            uint nXRayAQTime;

            var smallparts = fld.ListSmallParticles;
            var bigparts = fld.ListBigParticles;


            var pStatus = m_Sample.GetMsrStatus();
           
         
            //// particle x-ray analysis
            ////=============================================
            curFldData.CreateXrayList(bigparts); // big particle using the full xray strategy.


            curFldData.CreateXrayList(smallparts); //small particle using the fast xray strategy
            var workmode = pXRayParam.GetScanMode();
            // get x-ray list (analysis) by particle features
            if (workmode == OTS_X_RAY_SCAN_MODE.FeatureMode)
            {
                nXRayAQTime = (uint)pXRayParam.GetMidAnalyAQTime();
                m_EDSHardwareMgr.GetXRayByFeatures(bigparts, nXRayAQTime, true);

            }
            else 
            {
                nXRayAQTime = (uint)pXRayParam.GetMidAnalyAQTime();
                m_EDSHardwareMgr.GetXRayByPoints(bigparts, nXRayAQTime, true);
            }
            
  
         



            nXRayAQTime = (uint)pXRayParam.GetFastXrayTime();

            // get x-ray list (analysis) by points
            m_EDSHardwareMgr.GetXRayByPoints(smallparts, nXRayAQTime, true);
     
            return ;
        }

        public void ParticleSpecialTreatment(CFieldDataClean 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>();   //std.map<COTSParticlePtr, int> mapPartXray = new std.map<COTSParticlePtr, int>();
            double edsTime = 0; //to store the EDSTime returned from the engine.
            var bigparts = fld.ListBigParticles;
          var  m_ClassifyEngine = new CClassifyEngine();
            for (int i = 0; i < bigparts.Count(); i++)
            {
                var engine = m_ClassifyEngine.GetParticleEngine(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_EDSHardwareMgr.GetXRayByFeatures(partsMax, edsTime, true);
        


            }
        }

        public override void ClassifyFieldParticles()
        {
           
            try
            {
                CFieldDataClean curFldDataCln = (CFieldDataClean)curFldData;
                string libname = m_Sample.GetMsrParams().GetSTDName();
                if (libname != "NoSTDDB")
                {
                   log.Info("Begin to classify big particles!Using " + libname);
                    var bigparts = curFldDataCln.ListBigParticles;
                    ClassifyQuantifyParticles(bigparts,libname);
                    var smallParts = curFldDataCln.ListSmallParticles;
                    ClassifyQuantifyParticles(smallParts, libname);
                 
                }
            }
            catch (Exception e)
		    {
                log.Info("calcu the particle image property or classify failed. "+e.Message);
            }


        }
        public override void ClassifyMergedParticles(List<COTSParticleClr> mergedParts)
        {
           
            try
            {
                   
                string libname = m_Sample.GetMsrParams().GetSTDName();
                if (libname != "NoSTDDB")
                {
                    log.Info("Begin to classify big particles!Using " + libname);
                    var bigparts = mergedParts;
                    ClassifyQuantifyParticles(bigparts, libname);
                       
                     

                }
            }
            catch (Exception e)
            {
                log.Info("calcu the particle image property or classify failed. " + e.Message);
            }

        

        }
        public void SaveFieldParticlesData()
        {
            StartSaveFileThread(curFldData);
        }

        public void GetOriginalParticles()
        {
            // measure status
            CMsrSampleStatus pStatus = m_Sample.GetMsrStatus();

   
           // get image process parameter
           CSampleParam pMsrParam = m_Sample.GetMsrParams();
            COTSImageProcParam pImgProcessParam = pMsrParam.GetImageProcessParam();
            var dPixelsize = m_Sample.CalculatePixelSize();
            // remove BES image background
            curFldData.RemoveImgBGAndGetParticles(pImgProcessParam, dPixelsize);
   

            // check if this is an empty image
            if (curFldData.NoParticle())
            { // empty fields
                log.Info("ImageProcess: empty field.");
                //return false;
            }
            return ;
        }
        public bool ClassifyQuantifyParticles(List<COTSParticleClr> a_listAnalysisParticles, string libname)// classify particles
        {


            int nSize = (int)a_listAnalysisParticles.Count();

            // go through all analysis particles
            for (int i = 0; i < nSize; ++i)
            {
                COTSParticleClr pParticle = a_listAnalysisParticles[i];
           
                IClassifyEngine engine = m_classifyEngine.GetParticleEngine(libname);
                if (!engine.Classify(pParticle))
                {
                    // invalid x-ray pointer.
                    log.Info("ClassifyParticle: can't identify the particle as any classified id.");
                    return false;
                }
            }
            
            return true;
        }
        public bool ClassifySmallParticles(List<COTSParticleClr> smallparts, string libname)
        {
            List<COTSParticleClr> a_listAnalysisParticles = smallparts;

            int nSize = (int)a_listAnalysisParticles.Count();

            // go through all analysis particles
            for (int i = 0; i < nSize; ++i)
            {
                COTSParticleClr pParticle = a_listAnalysisParticles[i];
               
                IClassifyEngine engine = m_classifyEngine.GetCurveCompareEngine(libname);
                if (!engine.Classify(pParticle))
                {
                    log.Info("ClassifyParticle: can't identify the particle as any inclusion.");
                    return false;
                }
            }
            return true;
        }

        public bool SaveFieldFiles(CFieldDataClean 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.Info("SaveFieldFiles: save BSE file failed.");
                return false;
            }

            // IncA Data list

            CIncAFileMgr pDBFileMgr = m_pSampleRstFile.DBFileMgr;



            //pDBFileMgr.BeginTransaction();
            pDBFileMgr.SaveStatusDataToDB();
            var fldDB = pDBFileMgr.GetFieldDB();
            fldDB.SaveAField(fldData.GetId(), fldData.GetOTSPosition(),fldData.SemPos);
            if (!pDBFileMgr.SaveIncADataToDB(fldData.GetListAnalysisParticles(), fldData.GetOTSPosition()))
            {
                log.Info("SaveFieldFiles: save inclusion file failed.");
                return false;
            }
            //save the xray data and element data.
            CPosXrayDBMgr PosXrayDBMgr = pDBFileMgr.GetPosXrayDBMgr();
            var m_listAnalysisPosXray = new List<CPosXrayClr>();
            foreach (var p in fldData.GetListAnalysisParticles())
            {
                m_listAnalysisPosXray.Add(p.GetXray());
            }

            if (!PosXrayDBMgr.SaveXray(m_listAnalysisPosXray, true))
            {
                log.Info("SaveFieldFiles: save analysis x-ray failed.");
                return false;
            }



            //save the small particle info 
            CSmallParticleInfoDB smallPartDB = pDBFileMgr.GetSmallParticleInfoDB();
            Dictionary<int, List<COTSParticleClr>> mapSmallParts = new Dictionary<int, List<COTSParticleClr>>();
            foreach (COTSParticleClr smallP in fldData.ListSmallParticles)
            {
                if (mapSmallParts.ContainsKey((int)smallP.GetType()))
                {
                    mapSmallParts[(int)smallP.GetType()].Add(smallP);
                }
                else
                {
                    var plist = new List<COTSParticleClr>();
                    plist.Add(smallP);
                    mapSmallParts.Add((int)smallP.GetType(), plist);

                }

            }
            List<CSmallParticleInfo> smallparts = new List<CSmallParticleInfo>();

            foreach (KeyValuePair<int, List<COTSParticleClr>> particles in mapSmallParts)
            {
                CSmallParticleInfo partInfo = new CSmallParticleInfo();
                partInfo.FieldId = particles.Value[0].GetFieldId();
                partInfo.AveGray = particles.Value[0].GetAveGray();
                partInfo.Quantity = (int)(particles.Value.Count / fldData.SmallParticlePercentage);
                partInfo.TypeId = particles.Key;
                partInfo.TypeColor = particles.Value[0].GetTypeColor();
                partInfo.TypeName = particles.Value[0].GetTypeName();
                double area = 0;
                foreach (var p in particles.Value)
                {
                    area += p.GetActualArea();
                }
                //partInfo.Area = Convert.ToInt32(area / f.SmallParticlePercentage);
                partInfo.Area =(int) area ;
                smallparts.Add(partInfo);
            }
            List<KeyValuePair<string, SQLiteParameter[]>> cmds = new List<KeyValuePair<string, SQLiteParameter[]>>();
            foreach (CSmallParticleInfo smallp in smallparts)
            {
              var cmd=  smallPartDB.SaveAKindOfSmallParticle(smallp, new CPosXrayClr(), new System.Drawing.Point(0, 0));
                cmds.Add(cmd);
            }

            pDBFileMgr.ExecuteNonQueryBatch(ref cmds);

            return true;
        }


    }
}