OTS/OTSIncAMeasureApp/1-OTSMeasure/Measure/ParamData/COTSMsrPrjResultData.cs

using OTSDataType;
using OTSModelSharp.ServiceCenter;
using OTSModelSharp.DTLBase;
using OTSModelSharp.ImageProcess;
using System;
using System.Collections.Generic;
using System.Drawing;
using System.IO;

using System.Windows.Forms;
using static OTSDataType.otsdataconst;
using System.Xml;
using OTSCLRINTERFACE;

using System.Data;

namespace OTSModelSharp
{
    public class COTSMsrPrjResultData
    {

        // SEM stage data
        CSEMStageData m_pSEMStageData;
        //// stage
        CStage m_pStage;

        // general parameter
        COTSGeneralParam m_GenParam;



        // sample list
        List<COTSSample> m_listSamples = new List<COTSSample>();

        List<CHoleBSEImg> m_listHoleBSEImg = new List<CHoleBSEImg>();

        bool m_bModify;

        // path name
        String m_strPathName;

        // working sample index
        int m_nWorkingSampeIndex;

        const String UNTITLED_FILE_NAME = "Untitled";

 
        const String SMPL_MSR_RESULT_FIELDS_FILE_SUBFOLDER = "FIELD_FILES";

        // Inclusion file name
        const String SMPL_MSR_RESULT_INCLUSION_FILE = "Inclusion.db";//put all the table in one db file so that report can make join query.


        private otsdataconst.OTS_SysType_ID systemTypeId;

        public OTS_SysType_ID SystemTypeId { get => systemTypeId; set => systemTypeId = value; }

        public COTSMsrPrjResultData()
        {
            Init();

        }

        // initialization
        public void Init()
        {

            m_listSamples.Clear();
            m_listHoleBSEImg.Clear();

            m_bModify = false;
            m_strPathName = "";
            m_nWorkingSampeIndex = -1;

        }

        // duplication
        public void Duplicate(COTSMsrPrjResultData a_oSource)
        {
            // initialization
            Init();

            // copy data over
            m_pSEMStageData = new CSEMStageData(a_oSource.m_pSEMStageData);
            m_pStage = new CStage(a_oSource.m_pStage);


            foreach (var pHoleBSEImg in a_oSource.m_listHoleBSEImg)
            {
                CHoleBSEImg pHoleBSEImgNew = (new CHoleBSEImg(pHoleBSEImg));
                m_listHoleBSEImg.Add(pHoleBSEImgNew);
            }
            foreach (var pSample in a_oSource.m_listSamples)
            {
                COTSSample pSampleNew = new COTSSample();
                m_listSamples.Add(pSampleNew);
            }

            m_bModify = a_oSource.m_bModify;
            m_strPathName = a_oSource.m_strPathName;
            m_nWorkingSampeIndex = a_oSource.m_nWorkingSampeIndex;
        }

        public void SetPathName(String a_strPathName) { m_strPathName = a_strPathName; }

        public bool Load(string strPathName)
        {

           
            Cleanup();

            // check if the file exist 
            if (!FileExists(strPathName))
            {
                // shouldn't happen, file does not exist

                return false;
            }
            //获取测量项目文件
            XmlDocument doc = new XmlDocument();
            //载入xml文件
            doc.Load(strPathName); 
            XmlNode root = doc.SelectSingleNode("XMLData");
            Serialize(false, doc, root);

            //设置测量项目文件路径
            m_strPathName = strPathName;
            //-------------
            foreach (var smpl in m_listSamples)
            {
                // get path of the pathname
                String strFilePath = GetFolderName(strPathName);
                if (strFilePath == "")
                {
                    // file path string is an empty string 
                    return false;
                }

                // field file sub folder string
                String strFieldFileSubFolder = strFilePath + "\\" + smpl.GetName() + "\\" + SMPL_MSR_RESULT_FIELDS_FILE_SUBFOLDER + "\\";

                // check if the field file sub folder exists
                if (!DirectoryExists(strFieldFileSubFolder))
                {// field files folder doesn't exist

                    continue;
                }

                String strIncAFilename = strFieldFileSubFolder + "\\" + SMPL_MSR_RESULT_INCLUSION_FILE;
                //CIncAFileMgr pIncAFileMgr = new CIncAFileMgr(strIncAFilename);
                List<COTSField> allMeasuredFlds = new List<COTSField>();
                CMsrSampleStatus poMsrStatus = new CMsrSampleStatus();
               
                CMsrResultItems poMsrResults = smpl.GetMsrResults();
                double aFldArea = smpl.CalculateAFieldArea();
                SetPathName(strIncAFilename);

                int w, h;
                smpl.GetBSESize(out w, out h);
                double pixelsize = smpl.CalculatePixelSize();


                if (GetAllFieldsFromDB(ref allMeasuredFlds,ref poMsrStatus, poMsrResults, aFldArea,new Size(w,h),pixelsize))
                {
                  
                   
                    var nodataFields = smpl.GetFieldsData();//there's only the field postion info in the xml file,so the initial filed has only postion info.
                    List<COTSField> allflddata = new List<COTSField>() ;//contains all the field 
                    //------------complete the infomation that doesn't contained in database-----
                   
                    foreach (var f in allMeasuredFlds)
                    {
                        f.SetPixelSize(pixelsize);
                        f.Width = w;
                        f.Height = h;
                        f.SetIsMeasureComplete(true);

                    }
                  //------------------------------
                    foreach (var emptyfld in nodataFields)
                    {
                        bool isMeasured = false;
                        foreach (var measuredField in allMeasuredFlds)
                        {
                            if (measuredField.PositionEquals(emptyfld))
                            {
                               
                                allflddata.Add(measuredField);
                                isMeasured = true;
                                break;
                            }
                        
                        }
                        if (!isMeasured)
                        {

                            allflddata.Add(emptyfld);
                        }


                    }
                    smpl.SetFieldsData(allflddata);
                    // file validation
                    smpl.SetMsrStatus(poMsrStatus);
                    smpl.SetMsrResults(poMsrResults);

                

                    // set pathname
                    SetPathName(strPathName);

                    // set working sample
                    if (m_listSamples.Count > 0)
                    {
                        m_nWorkingSampeIndex = 0;
                    }
                    else
                    {
                        m_nWorkingSampeIndex = -1;
                    }


                }
                else
                {
                    return false;
                }
            }
            if (m_listSamples != null)
            {
                if (m_listSamples.Count > 0)
                {
                    m_nWorkingSampeIndex = 0;
                }
            }
            //-----------------------------------------
            return true;

        }

        // gets the name of the folder
        public String GetFolderName(String a_strPathName)
        {
            string str = "";

            str = Path.GetDirectoryName(a_strPathName);
            return str.ToString();
        }


        public bool FileExists(string a_sPath)
        {
            bool b_IsExists = File.Exists(a_sPath);
            return b_IsExists;
        }

        public bool DirectoryExists(string a_sPath)
        {
            bool b_IsExists = Directory.Exists(a_sPath);
            return b_IsExists;
        }
        // cleanup 
        public void Cleanup()
        {
            m_listHoleBSEImg.Clear();
            m_listSamples.Clear();

            m_bModify = false;
            m_strPathName = "";
            m_nWorkingSampeIndex = -1;
        }

        // set modify flag
        public void SetModify(bool a_bModify = true) { m_bModify = a_bModify; }

        // file pathname
        public String GetPathName() { return m_strPathName; }

        public bool GetAllFieldsFromDB(ref List<COTSField> allFlds, ref CMsrSampleStatus status, CMsrResultItems rst, double aFieldArea,Size picSize,double pixelSize)
        {
            String sDatabaseName = m_strPathName;

            if (!FileExists(sDatabaseName))
            {
                return false;

            }
            List<System.Drawing.PointF> completedFldPositions = new List<System.Drawing.PointF>();
            CIncAFileMgr incAFileMgr = new CIncAFileMgr(sDatabaseName);
            var m_IncADataDB = incAFileMgr.GetIncADB();
            List<COTSField> allFldsWithdata=new List<COTSField>();
            m_IncADataDB.GetAllFieldsRecord(ref allFldsWithdata);


            foreach (var f in allFldsWithdata)
            {
                f.Width = picSize.Width;
                f.Height = picSize.Height;
                f.SetPixelSize(pixelSize);
            
            }

            var eleChemistryDB = incAFileMgr.GetPosXrayDBMgr().GetElementChemistryDB();
             Dictionary<string, CPosXrayClr> mapXrayInfo=new Dictionary<string, CPosXrayClr>();
            eleChemistryDB.GetAllMapedXrayInfo(ref mapXrayInfo);
            foreach (var f in allFldsWithdata)
            {
                foreach (var p in f.GetListAnalysisParticles())
                {
                    int curFldId = f.GetId();
                    int xrayId = p.GetAnalysisId();
                    string fldvec="";
                    fldvec+=curFldId.ToString();
                    fldvec+="_";
                    fldvec += xrayId.ToString();
                    
                    if (mapXrayInfo.ContainsKey(fldvec))
                    {
                        var xray = mapXrayInfo[fldvec];
                     
                        p.SetXray(xray);
                    }
                }
            }


            var xrayDataDBDB = incAFileMgr.GetPosXrayDBMgr().GetXrayDataDB();
            Dictionary<string, CPosXrayClr> mapXrayData=new Dictionary<string, CPosXrayClr>();// map structure:[(fieldId,xrayId),CPosXrayPtr],every element of this map represent one unique xraydata.
            xrayDataDBDB.GetAllMapedXrayData(ref mapXrayData);
            foreach (var f in allFldsWithdata)
            {
                foreach (var p in f.GetListAnalysisParticles())
                {
                    int curFldId = f.GetId();
                    int xrayId = p.GetAnalysisId();
                    string fldvec="";
                    fldvec+=curFldId.ToString();
                    fldvec += "_";
                    fldvec += xrayId.ToString();
                  
                    if (mapXrayData.ContainsKey(fldvec))
                    {
                        var xray = mapXrayData[fldvec];
                        CPosXrayClr t2 = p.GetXray();
                        if (t2 == null)
                        {
                            t2 =new CPosXrayClr();
                            p.SetXray(t2);
                        }
                        t2.SetXrayData(xray.GetXrayData());

                    }
                }
            }


            CSegmentDB SegmentDB = incAFileMgr.GetSegmentDB();
            double msrFldsArea = 0;
           Dictionary<int, List<COTSParticleClr>> mapTypeParticles = new Dictionary<int,List<COTSParticleClr>>();//record typeId relevants particlelist;

            List<COTSSegmentClr> AllSegments ;
            Dictionary<string, List<COTSSegmentClr>> mapSegments = new Dictionary<string, List<COTSSegmentClr>>();
            if (SegmentDB.GetAllSegmentsRecord(mapSegments))
            {
               
                foreach (var fld in allFldsWithdata)
                {
                    int fldId = fld.GetId();
                    List<COTSParticleClr> parts = fld.GetListAnalysisParticles();
                    foreach (var part in parts)
                    {
                        string fldvec = "";
                        fldvec+=fldId.ToString();
                        fldvec += "_";
                        fldvec+=part.GetParticleId().ToString();

                       
                        if (mapSegments.ContainsKey(fldvec))
                        {
                            COTSFeatureClr f = new COTSFeatureClr();
                            AllSegments = mapSegments[fldvec];
                            f.SetSegmentsList(AllSegments, true);
                            part.SetFeature(f);
                         
                            if (mapTypeParticles.ContainsKey(part.GetType()))
                            {
                                mapTypeParticles[part.GetType()].Add(part);
                            }
                            else 
                            {
                                List<COTSParticleClr> ps = new List<COTSParticleClr>();
                                ps.Add(part);
                                mapTypeParticles.Add(part.GetType(), ps);
                            }
                           
                        }
                       
                        msrFldsArea += aFieldArea;
                    }
                


                }
            }

            var fielddb = incAFileMgr.GetFieldDB();
                var fielddata = fielddb.GetTableQueryForDataTable();

                foreach (DataRow r in fielddata.Rows)
                {
                    var p = new Point(Convert.ToInt32(r[(int)CFieldTable.ColumnID.N_FIELDPOS_X]), Convert.ToInt32(r[(int)CFieldTable.ColumnID.N_FIELDPOS_Y]));
                    completedFldPositions.Add(p);
                }

                status.SetCompletedFieldsCenter(completedFldPositions);


            //add the empty field(there's no any particle in the bse image,so the field empty)
            foreach (var p in completedFldPositions)
            {
                bool haveData=false;
                var emptyFld = new COTSField();
                emptyFld.SetOTSPosition(p);
                foreach (var fld in allFldsWithdata)
                {
                    
                    if (fld.PositionEquals(emptyFld))
                    {
                        haveData = true;
                        allFlds.Add(fld);
                        break;
                    }
                
                }
                if (!haveData)
                {
                    allFlds.Add(emptyFld);
                }
            
            
            }

                // get MsrStatus info from DB.
                var m_GenInfoDB = incAFileMgr.GetGeneralInfoDB();//DBStoreFile类
                String strTimeStart = "";
                String strTimeEnd = "";
                String strRstStatus = "";

                m_GenInfoDB.GetStringValue(m_GenInfoDB.GetTableItemNameTimeStart(), ref strTimeStart);
                m_GenInfoDB.GetStringValue(m_GenInfoDB.GetTableItemNameTimeEnd(), ref strTimeEnd);
                m_GenInfoDB.GetStringValue(m_GenInfoDB.GetTableItemNameResultStatus(), ref strRstStatus);
               
              

                DateTime timeStart, timeEnd;
                try
                {
                    timeStart = Convert.ToDateTime(ConvertFormatOfDateString(strTimeStart)); //此处为兼容之前得测量得结果可以打开，故在此进行数据格式变换
                    timeEnd = Convert.ToDateTime(ConvertFormatOfDateString(strTimeEnd));
                }
                catch
                {
                    timeStart = Convert.ToDateTime(strTimeStart); //此处为兼容之前得测量得结果可以打开，故在此进行数据格式变换
                    timeEnd = Convert.ToDateTime(strTimeEnd);
                }
                status.SetStartTime(timeStart);
                status.SetEndTime(timeEnd);
                status.SetUsedTime(timeEnd - timeStart);
                status.SetStatus((OTS_MSR_SAMPLE_STATUS)Convert.ToInt32(strRstStatus));

                //get MsrResults data from map.
                List<CMsrResultItem> rstItms = new List<CMsrResultItem>();
                double allPartArea = 0;
                int typeNum = 0;
                double typeArea = 0;
                foreach (var typeParticles in mapTypeParticles)
                {

                    CMsrResultItem rstItm = new CMsrResultItem();
                    foreach (var p in typeParticles.Value)
                    {
                        typeNum += 1;
                        typeArea +=p.GetActualArea();
                    }
                    rstItm.SetTypeId(typeParticles.Key);
                    rstItm.SetNumber((uint)typeNum);
                    rstItm.SetArea((uint)typeArea);
                    rstItm.SetName(typeParticles.Value[0].GetTypeName());
                    rstItms.Add(rstItm);
                    allPartArea += typeArea;
                }
                rst.SetResultItems(rstItms);
                rst.SetMeasuredArea(Convert.ToUInt64(msrFldsArea * 1000000));
                rst.SetRatio(allPartArea / (msrFldsArea * 1000000));
                return true;
            
            //return false;
        }

        string ConvertFormatOfDateString(string Time)
        {
            
            string[] str1 = Time.Split(' ');
           
            string[] str2 = str1[0].Split('/');
            return str2[2] + "/" + str2[1] + "/" + str2[0] +" "+ str1[1];
        }
        public string GetSampleWorkingFolder(string sampleName)
        {
            var pathname = FileHelper.GetFolderName(GetPathName());

            var samplePathName = pathname + "\\" + sampleName + "\\";
            return samplePathName;
        }
        public bool Save()
        {
            // Save or Save As, if strPathName is not empty, it is exist in the computer, this is a save action
            String strPathName = GetPathName();

            
            if (strPathName.CompareTo(UNTITLED_FILE_NAME) == 0)
            {
                // this is a new file 

                // return save as result
                return SaveAs();
            }
            // is this a new file?
            strPathName.Trim();
            //保存测量项目文件 .prj
            XmlDocument doc = new XmlDocument();
            doc.Load(strPathName);
            doc.RemoveAll();
            //添加xml文件头申明
            XmlDeclaration xmldecl = doc.CreateXmlDeclaration("1.0", "UTF-8", null);
            doc.AppendChild(xmldecl);
            XmlElement rootNode = doc.CreateElement("XMLData");
            doc.AppendChild(rootNode);

            Serialize(true, doc, rootNode);
            try
            {
                doc.Save(strPathName);
            }
            catch
            {
                return false;
            }

            // set file modify flag
            SetModify(false);

            // Ok, return TRUE
            return true;
        }

        public bool SaveAs()
        {
            // get file name
            String strPathName = "";
            // file open dialog
            SaveFileDialog saveFileDialog = new SaveFileDialog();
            saveFileDialog.FileName = m_strPathName.Split('\\')[m_strPathName.Split('\\').Length - 1];
            saveFileDialog.Filter = "Directory (*.*)|*.*";
            saveFileDialog.AddExtension=false;
            if (saveFileDialog.ShowDialog() != DialogResult.OK)
            {
                return false;

            }
            // get file pathname
            strPathName = saveFileDialog.FileName;
            string DirectoryName = Path.GetDirectoryName(strPathName);
            try
            {
                Directory.CreateDirectory(strPathName);
            }
            catch
            {
                MessageBox.Show("CreateDirectoryFailed!");
                return false;
            }
            strPathName += "\\"+Path.GetFileNameWithoutExtension(strPathName) + ".prj";
            //保存测量项目文件 .prj
            XmlDocument doc = new XmlDocument();
            //添加xml文件头申明
            XmlDeclaration xmldecl = doc.CreateXmlDeclaration("1.0", "UTF-8", null);
            doc.AppendChild(xmldecl);
            XmlElement rootNode = doc.CreateElement("XMLData");
            doc.AppendChild(rootNode);

            Serialize(true, doc, rootNode);
            try
            {
                doc.Save(strPathName);
            }
            catch
            {
                return false;
            }
            // set file modify flag
            m_bModify = false;

            // Set project Path
            SetPathName(strPathName);

            // Ok, return TRUE
            return true;
        }



        // SEM stage data
        public CSEMStageData GetSEMStageData() { return m_pSEMStageData; }

        // SEM stage data
        public void SetSEMStageData(CSEMStageData a_pCSEMStageData)
        {
            m_pSEMStageData = a_pCSEMStageData;
        }

        // stage
        public CStage GetStage() { return m_pStage; }
        public void SetStage(CStage a_pStage)
        {
            m_pStage = new CStage(a_pStage);
        }

        // samples list
        public List<COTSSample> GetSampleList() { return m_listSamples; }

 

        public COTSSample GetSampleByIndex(int a_nIndex)
        {
            // safe check
            if (a_nIndex < 0 || a_nIndex >= (int)m_listSamples.Count)
            {
                // invalid sample id

                return null;
            }
            // get the matching sample
            COTSSample pSample = m_listSamples[a_nIndex];

            // return the sample
            return pSample;
        }

        public COTSSample GetSampleByName(String a_strSampleName)
        {

            bool Isfind = false;
            COTSSample pOTSSample = null;
            for (int itr = 0; itr < m_listSamples.Count; itr++)
            {
                if (m_listSamples[itr].GetName() == a_strSampleName)
                {
                    pOTSSample = m_listSamples[itr];
                    //m_listSamples.RemoveAt(itr);
                    Isfind = true;
                }
            }

            if (Isfind)
            {
                return pOTSSample;
            }

            return m_listSamples[0];

        }

        public void AddSample(COTSSample pSample)
        {



            // add the new sample into the samples list
            m_listSamples.Add(pSample);

            // set the project file modified.
            SetModify();

            // set the new as working sample
            m_nWorkingSampeIndex = (int)m_listSamples.Count - 1;

            // return the new sample

        }





        // get new sample name




        public bool DeleteSampleByIndex(int a_nIndex)
        {
            // check the index
            if (a_nIndex < 0 || a_nIndex >= (int)m_listSamples.Count)
            {
                // invalid input sample index

                return true;
            }

            // calculate new working sample index
            int nNewWorkingSampeIndex;
            if (a_nIndex < m_nWorkingSampeIndex)
            {
                nNewWorkingSampeIndex = m_nWorkingSampeIndex - 1;
            }
            else if (a_nIndex > m_nWorkingSampeIndex)
            {
                nNewWorkingSampeIndex = m_nWorkingSampeIndex;
            }
            else
            {
                // deleting working sample.
                if (a_nIndex == (int)m_listSamples.Count - 1)
                {
                    // this is the last sample, select the above sample as working sample 
                    // if this is only sample in the list working sample index will be -1;
                    nNewWorkingSampeIndex = m_nWorkingSampeIndex - 1;
                }
                else
                {
                    // select next sample as working sample
                    nNewWorkingSampeIndex = m_nWorkingSampeIndex;
                }
            }

            // delete the sample 

            for (int i = m_listSamples.Count - 1; i >= 0; i--)
            {
                if (i == a_nIndex)
                {
                    var sam = m_listSamples[i];
                    sam.GetMsrStatus().ClearCompletedFieldsInfo();
                    sam.GetMsrStatus().ClearCompletedFieldsInfo();
                    sam.ClearFields();
                    sam.GetMsrStatus().SetStatus(OTS_MSR_SAMPLE_STATUS.UNMEASURED);
                    m_listSamples.Remove(m_listSamples[i]);
                    break;
                }
            }

            // the file is modified.
            SetModify();

            // reset working sample index
            m_nWorkingSampeIndex = nNewWorkingSampeIndex;

            // ok, return TRUE
            return true;
        }

        public bool ChangeParamFromList(int iNamePos)
        {
            throw new NotImplementedException();
        }

        public bool GetParamFileList(ref int iNamePos, ref List<string> mParamFileNameList)
        {
            throw new NotImplementedException();
        }

        public bool DeleteSampleByName(String a_strSampleName)
        {
            // check input sample name
            a_strSampleName.Trim();
            if (a_strSampleName == "")
            {
                // input sample name is empty

                return false;
            }

            // go through sample list
            int nIndex = 0;
            foreach (var pSample in m_listSamples)
            {
                // return TRUE if this is not an exclude sample and its name is same with input
                String strSampleName = pSample.GetName();
                if (strSampleName.CompareTo(a_strSampleName) == 0)
                {
                    // find the sample, return deleting result
                    return DeleteSampleByIndex(nIndex);
                }

                ++nIndex;
            }

            // can't find the sample in the samples list, return FALSE
            return false;
        }

        public bool ResetSamplesListOrder(List<String> a_listSampleNames)
        {
            // no sample in the samples list; shouldn't be here
            if (m_listSamples.Count == 0)
            {

                return false;
            }

            // make sure that input sample names list size is same with the samples list
            if (m_listSamples.Count != a_listSampleNames.Count)
            {

                return false;
            }

            // new sample list
            List<COTSSample> listSamples = new List<COTSSample>();

            // go through the sample names list
            foreach (var strSampleName in a_listSampleNames)
            {

                bool IsChanged = false;
                for (int itr = 0; itr < m_listSamples.Count; itr++)
                {
                    if (m_listSamples[itr].GetName() == strSampleName)
                    {
                        COTSSample pElementChemistry = m_listSamples[itr];

                        IsChanged = true;
                    }
                }

                if (!IsChanged)
                {
                    return false;
                }

            }

            // reset the samples list
            m_listSamples.Clear();
            foreach (var pSample in listSamples)
            {
                m_listSamples.Add(pSample);
            }

            // set modify flag
            SetModify();

            // Ok, return TRUE
            return true;
        }

        public bool InsrtSample(COTSSample a_pSample, int a_nIndex)
        {
            // input check

            if (a_pSample != null)
            {
                // invalid input sample pointer 

                return false;
            }
            if (m_listSamples.Count == 0 || a_nIndex >= (int)m_listSamples.Count)
            {
                m_listSamples.Add(a_pSample);
            }
            else if (a_nIndex <= 0)
            {
                m_listSamples.Insert(Convert.ToInt32(m_listSamples[a_nIndex]), a_pSample);
            }
            else
            {
                m_listSamples.Insert(Convert.ToInt32(m_listSamples[a_nIndex]) + a_nIndex, a_pSample);
            }

            // Ok, return TRUE
            return true;
        }

        public bool ChangeSamplePosition(int a_nIndexFrom, int a_nIndexTo)
        {
            // make sure both index are valid
            if (a_nIndexFrom < 0 || a_nIndexFrom >= (int)m_listSamples.Count)
            {
                // invalid from index                
                return false;
            }
            if (a_nIndexTo < 0 || a_nIndexTo >= (int)m_listSamples.Count)
            {
                // invalid to index             
                return false;
            }

            // need to do nothing if the two indexes are the same
            if (a_nIndexFrom != a_nIndexTo)
            {
                // move to last?
                bool bLast = (a_nIndexTo == ((int)m_listSamples.Count - 1));

                // get the sample 
                COTSSample pSample = m_listSamples[a_nIndexFrom];

                // remove it from the samples list
                m_listSamples.Remove(pSample);

                // put the sample back in 
                if (bLast)
                {
                    m_listSamples.Add(pSample);
                }
                else
                {
                    m_listSamples.Insert(Convert.ToInt32(m_listSamples[a_nIndexTo]) + a_nIndexTo, pSample);
                }
            }

            // Ok, return TRUE
            return true;
        }

        public bool MoveSamplePosition(COTSSample a_pTargetSample, COTSSample a_RefpSample, bool a_bBefore /*= TRUE*/)
        {
            // check input

            if (a_pTargetSample != null)
            {
                // invalid input target sample pointer 

                return false;
            }

            if (a_RefpSample != null)
            {
                // invalid input ref sample pointer 

                return false;
            }

            bool IsChanged = false;
            for (int itr = 0; itr < m_listSamples.Count; itr++)
            {
                if (m_listSamples[itr].GetName() == a_pTargetSample.GetName())
                {
                    COTSSample pElementChemistry = m_listSamples[itr];
                    // m_listSamples.RemoveAt(itr);
                    IsChanged = true;
                }
            }

            if (!IsChanged)
            {
                return false;
            }

            for (int itr = 0; itr < m_listSamples.Count; itr++)
            {
                if (m_listSamples[itr].GetName() == a_RefpSample.GetName())
                {
                    COTSSample pElementChemistry = m_listSamples[itr];
                    //m_listSamples.RemoveAt(itr);
                    IsChanged = true;
                }
            }

            if (!IsChanged)
            {
                return false;
            }

            // remove the sample from the samples list

            for (int itr = 0; itr < m_listSamples.Count; itr++)
            {
                if (m_listSamples[itr].GetName() == a_RefpSample.GetName())
                {
                    COTSSample pElementChemistry = m_listSamples[itr];
                    //m_listSamples.RemoveAt(itr);
                    IsChanged = true;
                }
            }

            if (!IsChanged)
            {
                return false;
            }
            // put the sample back in 
            if (a_bBefore)
            {
                m_listSamples.Insert(0, a_pTargetSample);
            }
            else
            {
                m_listSamples.Insert(1, a_pTargetSample);
            }

            // Ok, return TRUE
            return true;
        }

        public bool MoveSamplePosition(String a_strTargetSampleName, String a_strRefSampleName, bool a_bBefore /*= TRUE*/)
        {
            // input check
            a_strTargetSampleName.Trim();
            if (a_strTargetSampleName == "")
            {
                // input target sample is an empty string 

                return false;
            }
            a_strRefSampleName.Trim();
            if (a_strRefSampleName == "")
            {
                // input ref sample is an empty string 

                return false;
            }

            bool IsChanged = false;
            for (int itr = 0; itr < m_listSamples.Count; itr++)
            {
                if (m_listSamples[itr].GetName() == a_strTargetSampleName)
                {
                    COTSSample pElementChemistry = m_listSamples[itr];
                    IsChanged = true;
                }
            }

            if (!IsChanged)
            {
                return false;
            }
            COTSSample pTargetSample = m_listSamples[0];


            for (int itr = 0; itr < m_listSamples.Count; itr++)
            {
                if (m_listSamples[itr].GetName() == a_strTargetSampleName)
                {
                    COTSSample pElementChemistry = m_listSamples[itr];

                    IsChanged = true;
                }
            }

            if (!IsChanged)
            {
                return false;
            }
            COTSSample pRefSample = pTargetSample;

            // need to do nothing if the two name are same
            if (a_strTargetSampleName.CompareTo(a_strRefSampleName) != 0)
            {
                return MoveSamplePosition(pTargetSample, pRefSample, a_bBefore);
            }

            // Ok, return TRUE
            return true;
        }

        public COTSSample GetWorkingSample()
        {
         
            return GetSampleByIndex(m_nWorkingSampeIndex);
        }

  

        public bool SetWorkingSampleByIndex(int a_nIndex)
        {
            // special treatment
            if (a_nIndex == -1 && m_listSamples.Count == 0)
            {
                m_nWorkingSampeIndex = -1;
                return true;
            }

            // check if the working sample index
            if (0 > a_nIndex || a_nIndex >= (int)m_listSamples.Count)
            {
                // invalid sample index
                return false;
            }

            m_nWorkingSampeIndex = a_nIndex;
            return true;
        }

        public bool SetWorkingSampleByName(String a_pSampleName)
        {
            // check input sample name
            a_pSampleName.Trim();
            if (a_pSampleName == "")
            {
                // input sample name is empty

                return false;
            }

            // go through sample list
            int nIndex = 0;
            foreach (var pSample in m_listSamples)
            {
                // return TRUE if this is not an exclude sample and its name is same with input
                String strSampleName = pSample.GetName();
                if (strSampleName.CompareTo(a_pSampleName) == 0)
                {
                    // find the sample, return deleting result
                    return SetWorkingSampleByIndex(nIndex);
                }

                ++nIndex;
            }

            // failed to find the named sample

            // failed to find the named sample return FALSE
            return false;
        }

        public bool DeleteWorkingSample()
        {
            // check if the working sample index
            if (m_nWorkingSampeIndex < 0 || m_nWorkingSampeIndex >= (int)m_listSamples.Count)
            {
                // invalid working sample index
                return false;
            }

            // return the result of DeleteSampleByIndex
            return DeleteSampleByIndex(m_nWorkingSampeIndex);
        }

        // Sample hole BSE image list
        public List<CHoleBSEImg> GetHoleBESImgList() { return m_listHoleBSEImg; }

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

            m_listHoleBSEImg = a_listHoleBSEImg;

           
        }

        // get modify flag
        public bool IsModified() { return m_bModify; }

        // file name
        public String GetFileName()
        {
            // make a copy of file path name
            String strPathName = m_strPathName;

            // is this a new file?           
            if (strPathName.CompareTo(UNTITLED_FILE_NAME) == 0)
            {
                return strPathName;
            }

            // get file name
            String strFileName = GetFileNameWithoutExtension(strPathName);


            // return file name
            return strFileName;
        }

        // get file name without extension
        public String GetFileNameWithoutExtension(String a_strPathName)
        {
            string str = "";
            str = Path.GetFileNameWithoutExtension(a_strPathName);
            return str;
        }

        // if the new sample name can be used.
        public bool IsValidSampleName(String a_sName)
        {
            foreach (var pSample in m_listSamples)
            {
               

                String sSampleName = pSample.GetName();
                if (a_sName.Equals(sSampleName))
                {
                    

                        return false;
                   
                }
            }

            return true;
        }

      

        static String FindFile(String filename, String path)
        {
            if (Directory.Exists(path))
            {
                if (File.Exists(path + filename))
                    return path + filename;
                String[] directorys = Directory.GetDirectories(path);
                foreach (String d in directorys)
                {
                    String p = FindFile(filename, d);
                    if (p != null)
                        return p;
                }
            }
            return null;
        }

       

        // get measured sample list
        public bool GetMsredSampleList(ref List<COTSSample> a_listMsredSample)
        {
            a_listMsredSample.Clear();

            foreach (var pSample in m_listSamples)
            {

                if (pSample.GetMsrResults() == new CMsrResultItems())
                {

                    continue;
                }
                else
                {

                    a_listMsredSample.Add(pSample);//the reference count will increament automatically.
                }
            }

            return true;
        }

        // calculate measurement area
        public CDomain CalculateMsrArea(CHole a_pHole)
        {
            CDomain pMsrArea = new CDomain(a_pHole.GetShape(), a_pHole.GetDomainRect());
            // create measurement area
            // reset measurement area 
            // measurement area should smaller than the sample hole
            RectangleF rectMsrArea = pMsrArea.GetDomainRect();
            float  nWidth = rectMsrArea.Width;
            float  nHeight = rectMsrArea.Height;
            float  nDeflateX = CalculateDeflateValue(nWidth);
            float  nDeflateY = CalculateDeflateValue(nHeight);
            rectMsrArea.Offset(nDeflateX, nDeflateY);
            pMsrArea.SetDomainRect(rectMsrArea);

            // return measurement area
            return pMsrArea;
        }

        // calculate deflate value
        public float  CalculateDeflateValue(float  a_nWitchOrHeight)
        {
            const long LENGTH_THRESHOLD = 150000;
            const long LENGTH_THRESHOLD_MIN = 10000;
            const int EDGE = 1000;
            const int EDGE_MIN = 500;
            // deflate 1000 if width or height is greater than 15000
            if (a_nWitchOrHeight >= LENGTH_THRESHOLD)
            {
                return EDGE;
            }
            // deflate 500 if width or height is greater than 15000
            else if (a_nWitchOrHeight >= LENGTH_THRESHOLD_MIN)
            {
                return EDGE_MIN;
            }

            // otherwise, no deflate
            return 0;
        }


        //合并后新添加的需要的方法
        public void SetGenParam(COTSGeneralParam GenParam) { m_GenParam = GenParam; }
        public COTSGeneralParam GetGenParam() { return m_GenParam; }

        public bool Reclassify()
        {
            
            string strFilePath = FileHelper.GetFolderName(m_strPathName);
            if(strFilePath==null)
            {
                return false;
            }

            foreach (var spl in m_listSamples)
            {

                //get the parameter MsrParam object
                CSampleParam pMsrParam = spl.GetMsrParams();
                string stdFileName = pMsrParam.GetSTDName();
                if (!stdFileName.Contains(".db"))
                {
                    stdFileName += ".db";
                }

                string filename = strFilePath + "\\" + spl.GetName() + "\\" + spl.GetName() + ".rst";
               
                XmlDocument doc=new XmlDocument();
                doc.Load(filename);

                XmlNode  root = doc.SelectSingleNode("XMLData");
               var members = root.SelectNodes("Member");
                foreach (XmlNode member1 in members)
                {
                    if(member1.Attributes["RegName"].Value== "Sample")
                    {
                        var paramNode = member1.SelectNodes("Member");
                        foreach (XmlNode member2 in paramNode)
                        {
                            if(member2.Attributes["RegName"].Value == "MsrParams")
                            {
                                ((XmlElement)member2).SetAttribute("STDName", stdFileName);
                            }
                        }
                    }
                }
                
                doc.Save(filename);
                foreach (var fld in spl.GetFieldsData())
                {
                    foreach (var part in fld.GetListAnalysisParticles())
                    {
                        
                        part.SetType((int)OTS_PARTICLE_TYPE.NOT_IDENTIFIED);
                        part.SetTypeName("Not Identified");
                        part.SetTypeColor("#000000");
                    }
                }
                var analysisparts = new List<COTSParticleClr>();
                var m_classifyEngine = new CClassifyEngine();
                if (SystemTypeId == OTS_SysType_ID.IncA)
                {
                    //get the steel technology parameter
                    STEEL_TECHNOLOGY steelTech = pMsrParam.GetSteelTechnology();
                    if (spl.GetMsrParams().GetSysSTDSwitch())
                    {
                        if (stdFileName != "NoSTDDB.db")
                        {
                            foreach (var fld in spl.GetFieldsData())
                            {
                                foreach (var part in fld.GetListAnalysisParticles())
                                {
                                    IClassifyEngine partEngine = m_classifyEngine.GetExpressionClassifyEngine(stdFileName);
                                    if (IsLowCounts(part))
                                    {
                                        continue;
                                    
                                    }
                                    if (!partEngine.ClassifyByExpression(part))
                                    {

                                        NLog.LogManager.GetCurrentClassLogger().Error("1 failed to classify!" + "Particle Engine");
                                    }


                                    if (part.GetType() == (int)OTS_PARTICLE_TYPE.NOT_IDENTIFIED)
                                    {

                                        IClassifyEngine incAEngine = m_classifyEngine.GetIncClassifyEngine();
                                        if (!incAEngine.ClassifyIncA(part, (int)steelTech))
                                        {

                                            NLog.LogManager.GetCurrentClassLogger().Error("2 failed to classify!" + "IncA Engine");
                                        }

                                    }

                                }
                                analysisparts.AddRange(fld.GetListAnalysisParticles());
                            }
                        }
                        else
                        {
                            foreach (var fld in spl.GetFieldsData())
                            {
                                foreach (var part in fld.GetListAnalysisParticles())
                                {
                                    if (IsLowCounts(part))
                                    {
                                        continue;

                                    }
                                    IClassifyEngine incAEngine = m_classifyEngine.GetIncClassifyEngine();
                                    if (!incAEngine.ClassifyIncA(part, (int)steelTech))
                                    {

                                        NLog.LogManager.GetCurrentClassLogger().Error("2 failed to classify!" + "IncA Engine");
                                    }
                                }
                                analysisparts.AddRange(fld.GetListAnalysisParticles());

                            }
                        }
                    }
                    else
                    {

                        if (stdFileName != "NoSTDDB.db")
                        {
                            foreach (var fld in spl.GetFieldsData())
                            {
                                foreach (var part in fld.GetListAnalysisParticles())
                                {
                                    if (IsLowCounts(part))
                                    {
                                        continue;

                                    }
                                    IClassifyEngine engine = m_classifyEngine.GetExpressionClassifyEngine(stdFileName);
                                    if (!engine.ClassifyByExpression(part))
                                    {

                                        NLog.LogManager.GetCurrentClassLogger().Error("3 failed to classify!" + "Particle Engine");
                                    }
                                }
                                analysisparts.AddRange(fld.GetListAnalysisParticles());
                            }
                        }
                    }

                }
                else if (SystemTypeId == OTS_SysType_ID.CleannessA)
                {
                    if (stdFileName != "NoSTDDB.db")
                    {
                        foreach (var fld in spl.GetFieldsData())
                        {
                            foreach (var part in fld.GetListAnalysisParticles())
                            {
                                if (IsLowCounts(part))
                                {
                                    continue;

                                }
                                IClassifyEngine engine = m_classifyEngine.GetExpressionClassifyEngine(stdFileName);
                                if (!engine.ClassifyByExpression(part))
                                {

                                    NLog.LogManager.GetCurrentClassLogger().Error("3 failed to classify!" + "Particle Engine");
                                }
                            }
                            analysisparts.AddRange(fld.GetListAnalysisParticles());

                        }
                    }

                }
                string strFieldFileSubFolder = strFilePath + "\\" + spl.GetName() + "\\" + SMPL_MSR_RESULT_FIELDS_FILE_SUBFOLDER;

                string strIncAFilename = strFieldFileSubFolder + "\\" + SMPL_MSR_RESULT_INCLUSION_FILE;
                CIncAFileMgr pIncAFileMgr = new CIncAFileMgr(strIncAFilename);


                pIncAFileMgr.UpdateParticleList(analysisparts);

                if (stdFileName.ToLower() != "nostddb.db")
                {
                    try
                    {
                        string userdBpath = Application.StartupPath + "\\Config\\SysData\\" + stdFileName;
                        File.Copy(userdBpath, strFilePath + "\\" + spl.GetName() + "\\" + stdFileName, true);
                    }
                    catch (Exception ex)
                    {
                        MessageBox.Show(stdFileName+" copy failed:" + ex.ToString());
                        return false;
                    }
                }
            }


            return true;




        }

        private bool IsLowCounts(COTSParticleClr particle)
        {
            COTSXRayParam pXRayParam = this.GetWorkingSample().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);//4 represent "lowcount"
                    particle.SetTypeColor("#000000");
                    particle.SetTypeName("LowCounts");
                    return true;
                }
            }
            return false;
        }



        /// <summary>
        /// 设置样品中对象属性 赋值
        /// </summary>
        /// <param name="pSample"></param>
        /// <param name="poMsrParams"></param>
        /// <returns></returns>


        void Serialize(bool isStoring, XmlDocument classDoc, XmlNode rootNode)
        {
           
            // copy data over
            if (m_pSEMStageData == null)
            {
                m_pSEMStageData = new CSEMStageData();
            }
            if (m_pStage == null)
            {
                m_pStage = new CStage();
            }
            xInt xProjMgrFileMark = new xInt();
            xString xProjMgrFileVersion = new xString();
            xString xstrPathName = new xString();
            xString xSystype = new xString();
            Collection<CHoleBSEImg> xholeBSEImgs = new Collection<CHoleBSEImg>();
            Collection<COTSSample> xsamples = new Collection<COTSSample>();
            Slo slo = new Slo();
            
            slo.Register("ProjMgrFileMark", xProjMgrFileMark);
            slo.Register("ProjMgrFileVersion", xProjMgrFileVersion);
            slo.Register("strPathName", xstrPathName);
            slo.Register("SysType", xSystype);
            slo.Register("SEMStageData", m_pSEMStageData);
            slo.Register("Stage", m_pStage);
            slo.Register("HoleBSEImg", xholeBSEImgs);
            slo.Register("Samples", xsamples);

            if (isStoring)
            {
                xProjMgrFileMark.AssignValue(0);
                xProjMgrFileVersion.AssignValue("");
                xSystype.AssignValue(systemTypeId.ToString());
                xstrPathName.AssignValue(m_strPathName);
                xholeBSEImgs.Clear();
             
                xsamples.Clear();
                foreach (var sample in m_listSamples)
                {
                    xsamples.addItem(sample);
                }
                slo.Serialize(true, classDoc, rootNode);

            }
            else
            {
                slo.Serialize(false, classDoc, rootNode);
                m_strPathName = xstrPathName.value();
                m_listHoleBSEImg.Clear();
              
                m_listSamples.Clear();
                for (int i = 0; i < (int)xsamples.size(); i++)
                {
                    m_listSamples.Add(xsamples.getItem(i));
                }
                if(xSystype.value()== "IncA")
                {
                    systemTypeId = otsdataconst.OTS_SysType_ID.IncA;
                }
                else 
                {
                    systemTypeId = otsdataconst.OTS_SysType_ID.CleannessA;
                }
            }

        }
    }
}