コード例 #1
0
ファイル: WindowHCSAnalyzer.cs プロジェクト: cyrenaique/HCSA
        private void simpleTestToolStripMenuItem_Click(object sender, EventArgs e)
        {
            Random RNd = new Random();

            int NumRow = 8;
            double InitialValue = 10;
            int NumCol = 12;


            cExtendedTable FinalTable = null;
            for (int Col = 1; Col <= NumCol; Col++)
            {


                for (int Repeat = 1; Repeat <= NumRow; Repeat++)
                {
                    cExtendedTable GeneratedTable = new cExtendedTable(1, 1000, InitialValue);

                    cAddNoise AN = new cAddNoise();
                    AN.DistributionType = eRandDistributionType.GAUSSIAN;
                    AN.Mean = 20;// Col*1.2;
                    AN.Stdv = 0.5 * Col;
                    AN.SetInputData(GeneratedTable);
                    AN.Run();
                    GeneratedTable = AN.GetOutPut();



                    //for (int i = 0; i < GeneratedTable[0].Count; i++)
                    //{
                    //    GeneratedTable[0][i] = Col;
                    //    GeneratedTable[1][i] = Repeat;
                    //}

                    GeneratedTable.ListRowNames = new List<string>();
                    for (int i = 0; i < GeneratedTable[0].Count; i++)
                    {
                        GeneratedTable.ListRowNames.Add(ConvertPosition(Col, Repeat));
                    }

                    if (FinalTable == null)
                        FinalTable = new cExtendedTable(GeneratedTable);
                    else
                    {
                        cMerge M = new cMerge();
                        M.IsHorizontal = false;
                        M.SetInputData(FinalTable, GeneratedTable);
                        M.Run();
                        FinalTable = M.GetOutPut();
                    }

                }


            }

            FinalTable.Name = "generated screen";
            FinalTable[0].Name = "Volume";
            //  FinalTable[1].Name = "Row";
            //  FinalTable[2].Name = "Volume";
            cDisplayExtendedTable DET = new cDisplayExtendedTable();
            //DET.SetInputData(FinalTable);
            //DET.Run();

            cTableToFile TTF = new cTableToFile();
            TTF.SetInputData(FinalTable);
            TTF.IsDisplayUIForFilePath = true;
            TTF.IsRunEXCEL = true;
            TTF.IsAppend = false;
            TTF.Run();



        }
コード例 #2
0
ファイル: cGetListPhenotypes.cs プロジェクト: cyrenaique/HCSA
        void Process()
        {
            // here is the core of the meta component ...
            // just a list of Component steps
            foreach (cWell item in Input)
            {
                item.AssociatedPlate.DBConnection = new cDBConnection(item.AssociatedPlate, item.SQLTableName);

                cListSingleBiologicalObjects ListPhenotypes = item.AssociatedPlate.DBConnection.GetBiologicalPhenotypes(item);

                cExtendedTable ET = item.AssociatedPlate.DBConnection.GetWellValues(item, cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptors());
                item.AssociatedPlate.DBConnection.CloseConnection();

                ET.ListTags = new List<object>();

                for (int i = 0; i < ET.Count; i++)
                {
                    ET[i].ListTags = new List<object>();

                    for (int j = 0; j < ListPhenotypes.Count; j++)
                        ET[i].ListTags.Add(ListPhenotypes[j]);
                }

                for (int j = 0; j < ListPhenotypes.Count; j++)
                    ET.ListTags.Add(ListPhenotypes[j]);

                if (Output == null)
                    Output = new cExtendedTable(ET);
                else
                {
                    cMerge M = new cMerge();
                    M.IsHorizontal = false;
                    M.SetInputData(Output, ET);
                    M.Run();

                    Output = M.GetOutPut();
                }
            }
        }
コード例 #3
0
ファイル: WindowHCSAnalyzer.cs プロジェクト: cyrenaique/HCSA
        private void drawSingleDRCToolStripMenuItem_Click(object sender, EventArgs e)
        {
            int NumberOfReplicate = 4;
            int DRCNumberofPoints = 20;

            cExtendedTable FullResults = new cExtendedTable();
            FullResults.ListRowNames = new List<string>();



            cExtendedList ListPValues = new cExtendedList("DRC");


            cDataGeneratorTitration GT = new cDataGeneratorTitration();
            GT.NumberOfPoint = DRCNumberofPoints;
            GT.Start = 100;
            GT.DilutionFactor = 3;
            GT.Run();


            Random RND = new Random();

            cExtendedTable FinalTable = new cExtendedTable();

            cDataGeneratorSigmoid DGS = null;
            DGS = new cDataGeneratorSigmoid();
            DGS.SetInputData(GT.GetOutPut()[0]);
            DGS.EC50 = 0.01;
            DGS.Bottom = 10;
            DGS.Top = 110;
            DGS.Slope = 1;
            DGS.Run();

            // cAddNoise AN = new cAddNoise();
            // AN.DistributionType = eRandDistributionType.GAUSSIAN;

            double NoiseLevel = 10;
            //   EXT[0].Add(NoiseLevel);
            //   EXT[1].Add(DGS.EC50);

            #region loop over the replicates
            for (int NumReplic = 0; NumReplic < NumberOfReplicate; NumReplic++)
            {

                cExtendedList NewL = DGS.GetOutPut()[1];
                for (int k = 0; k < NewL.Count; k++)
                {
                    NewL[k] += RND.NextDouble() * NoiseLevel;
                }

                cExtendedTable TmpTable = new cExtendedTable();
                TmpTable.Add(GT.GetOutPut()[0]);
                TmpTable.Add(NewL);

                if (NumReplic >= 1)
                {
                    cMerge M = new cMerge();
                    M.IsHorizontal = false;
                    M.SetInputData(TmpTable, FinalTable);
                    M.Run();
                    FinalTable = M.GetOutPut();
                }
                else
                    FinalTable = new cExtendedTable(TmpTable);

            }
            #endregion


            cSigmoidFitting SF = new cSigmoidFitting();
            SF.SetInputData(FinalTable);
            SF.Run();

            cGlobalInfo.ConsoleWriteLine("Slope :" + DGS.Slope + " - Evaluated:" + SF.GetOutPut()[0][3]);
            cGlobalInfo.ConsoleWriteLine("Top :" + DGS.Top + " - Evaluated:" + SF.GetOutPut()[0][1]);
            cGlobalInfo.ConsoleWriteLine("Bottom :" + DGS.Bottom + " - Evaluated:" + SF.GetOutPut()[0][0]);
            cGlobalInfo.ConsoleWriteLine("EC50 :" + DGS.EC50 + " - Evaluated:" + SF.GetOutPut()[0][2]);


            // return;


            cCurveForGraph CFG = new cCurveForGraph();
            CFG.SetInputData(FinalTable);
            CFG.Run();

            cExtendedTable Sigmoid = SF.GetFittedRawValues(GT.GetOutPut()[0]);
            FinalTable[0] = Sigmoid[1];


            cViewerGraph1D VS1 = new cViewerGraph1D();
            VS1.SetInputData(new cExtendedTable(Sigmoid[1]));
            VS1.AddCurve(CFG);
            VS1.Chart.X_AxisValues = Sigmoid[0];//DGS.GetOutPut()[0];
            VS1.Chart.IsLogAxis = true;
            VS1.Chart.IsLine = true;
            VS1.Chart.IsShadow = true;
            VS1.Chart.Opacity = 210;
            VS1.Chart.LineWidth = 3;
            VS1.Chart.LabelAxisX = "Concentration";
            VS1.Chart.LabelAxisY = "Readout";
            VS1.Chart.XAxisFormatDigitNumber = -1;
            VS1.Chart.IsZoomableX = true;
            VS1.Chart.IsZoomableY = true;
            VS1.Run();

            cDesignerSinglePanel CD = new cDesignerSinglePanel();
            CD.SetInputData(VS1.GetOutPut());
            CD.Run();

            cDisplayToWindow DTW = new cDisplayToWindow();
            DTW.SetInputData(CD.GetOutPut());//DS.GetOutPut());
            DTW.Run();
            DTW.Display();

        }
コード例 #4
0
ファイル: WindowHCSAnalyzer.cs プロジェクト: cyrenaique/HCSA
        private void sigmoidFittToolStripMenuItem_Click(object sender, EventArgs e)
        {

            int NumberOfReplicate = 4;
            int NumberOfCurves = 30;
            int DRCNumberofPoints = 12;

            cExtendedTable FullResults = new cExtendedTable();
            FullResults.ListRowNames = new List<string>();

            double RealEC50 = 0.0001;
            int NumberOfDiffEC50 = 20;
            int NumberOfSlopes = 100;

            //  for (int EC50 = 0; EC50 < NumberOfDiffEC50; EC50++)
            {




                //double TmpSlopeValue = 0.0;
                for (int EC50 = 0; EC50 < NumberOfDiffEC50; EC50++)
                //for (int SlopeTmp = 0; SlopeTmp < NumberOfSlopes; SlopeTmp++)
                {
                    RealEC50 *= 2;
                    //TmpSlopeValue += 0.1;
                    cExtendedList ListPValues = new cExtendedList("EC50 - " + RealEC50/*TmpSlopeValue*/);


                    cDesignerTab DT = new cDesignerTab();
                    DT.IsMultiline = false;

                    cDataGeneratorTitration GT = new cDataGeneratorTitration();
                    GT.NumberOfPoint = DRCNumberofPoints;
                    GT.Start = 5;
                    GT.DilutionFactor = 2;
                    GT.Run();


                    Random RND = new Random();

                    //cExtendedTable EXT = new cExtendedTable();
                    //EXT.ListRowNames = new List<string>();
                    //EXT.Name = "Quality fitting Report";
                    //EXT.Add(new cExtendedList("Noise Level"));
                    //EXT.Add(new cExtendedList("Original EC50"));
                    //EXT.Add(new cExtendedList("Estimated EC50"));
                    //EXT.Add(new cExtendedList("p-Value"));

                    for (int i = 0; i < NumberOfCurves; i++)
                    {
                        cExtendedTable FinalTable = new cExtendedTable();

                        cDataGeneratorSigmoid DGS = null;
                        DGS = new cDataGeneratorSigmoid();
                        DGS.SetInputData(GT.GetOutPut()[0]);
                        DGS.EC50 = RealEC50;// 0.01;// 1;// 0.1;// Math.Pow((double)10, -2);
                        DGS.Bottom = 0;
                        DGS.Top = 100;
                        DGS.Slope = 2;// TmpSlopeValue;//1;
                        DGS.Run();

                        cAddNoise AN = new cAddNoise();
                        AN.DistributionType = eRandDistributionType.GAUSSIAN;

                        double NoiseLevel = (i + 1) * 5;
                        //   EXT[0].Add(NoiseLevel);
                        //   EXT[1].Add(DGS.EC50);

                        #region loop over the replicates
                        for (int NumReplic = 0; NumReplic < NumberOfReplicate; NumReplic++)
                        {
                            //AN.Mean = 0;
                            //AN.Stdv = 10;

                            //AN.SetInputData(DGS.GetOutPut());
                            //AN.Run();

                            cExtendedList NewL = DGS.GetOutPut()[1];
                            for (int k = 0; k < NewL.Count; k++)
                            {
                                NewL[k] += RND.NextDouble() * NoiseLevel;
                            }

                            cExtendedTable TmpTable = new cExtendedTable();
                            TmpTable.Add(GT.GetOutPut()[0]);
                            TmpTable.Add(/*AN.GetOutPut()[1]*/NewL);

                            if (NumReplic >= 1)
                            {
                                cMerge M = new cMerge();
                                M.IsHorizontal = false;
                                M.SetInputData(TmpTable, FinalTable);
                                M.Run();
                                FinalTable = M.GetOutPut();
                            }
                            else
                                FinalTable = new cExtendedTable(TmpTable);

                        }
                        #endregion

                        //cListWell LW = new cListWell(null);
                        //foreach (cWell item in CompleteScreening.GetCurrentDisplayPlate().ListActiveWells)
                        //{
                        //    if (item.GetClassIdx() == 0)
                        //        LW.Add(item);
                        //}
                        //cExtendedTable ET = LW.GetDescriptorValues(CompleteScreening.ListDescriptors.GetActiveDescriptors(), true);


                        cCurveForGraph CFG = new cCurveForGraph();
                        CFG.SetInputData(FinalTable);
                        CFG.Run();

                        // compute ANOVA
                        cANOVA S = new cANOVA();
                        cExtendedTable NewTable = CFG.ListPtValues.Crop(0, CFG.ListPtValues.Count - 1, 1, CFG.ListPtValues[0].Count - 1);
                        S.SignificanceThreshold = 1E-11;
                        S.SetInputData(NewTable);
                        S.Run();

                        //cLinearRegression LR = new cLinearRegression();
                        //LR.SetInputData(FinalTable);
                        //LR.Run();

                        cSigmoidFitting SF = new cSigmoidFitting();
                        SF.SetInputData(FinalTable);
                        if (SF.Run().IsSucceed == false) continue;

                        // double Ratio = LR.GetOutPut()[0][LR.GetOutPut().Count - 1] / SF.GetOutPut()[0][SF.GetOutPut().Count - 1];


                        cExtendedTable Sigmoid = SF.GetFittedRawValues(GT.GetOutPut()[0]);
                        FinalTable[0] = Sigmoid[1];

                        cDesignerSplitter DS = new cDesignerSplitter();

                        ////cViewerTableAsRichText VT = new cViewerTableAsRichText();
                        cViewerTable VT = new cViewerTable();
                        cExtendedTable TableResults = SF.GetOutPut();
                        TableResults[0].Add(S.GetOutPut()[0][0]);

                        ListPValues.Add(S.GetOutPut()[0][0]);

                        TableResults[0].Add(S.GetOutPut()[0][1]);
                        TableResults.ListRowNames.Add("p-Value");
                        TableResults.ListRowNames.Add("Null hyp. rejected?");

                        VT.SetInputData(TableResults);
                        VT.DigitNumber = -1;
                        VT.Run();

                        cViewerGraph1D VS1 = new cViewerGraph1D();

                        VS1.SetInputData(new cExtendedTable(Sigmoid[1]));

                        VS1.AddCurve(CFG);

                        VS1.Chart.X_AxisValues = Sigmoid[0];//DGS.GetOutPut()[0];
                        VS1.Chart.IsLogAxis = true;
                        VS1.Chart.IsLine = true;
                        VS1.Chart.IsShadow = true;
                        VS1.Chart.Opacity = 210;
                        VS1.Chart.LineWidth = 3;

                        VS1.Chart.LabelAxisX = "Concentration";
                        VS1.Chart.LabelAxisY = "Readout";
                        VS1.Chart.XAxisFormatDigitNumber = -1;
                        VS1.Chart.IsZoomableX = true;

                        //Classes.Base_Classes.General.cLineVerticalForGraph VLForEC50 = new Classes.Base_Classes.General.cLineVerticalForGraph(SF.GetOutPut()[0][2]);
                        //VLForEC50.AddText("EC50: " + SF.GetOutPut()[0][2].ToString("e3")/* + "\nError Ratio:" + Ratio.ToString("N4")*/);
                        //VS1.Chart.ListVerticalLines.Add(VLForEC50);
                        //VS1.Chart.ArraySeriesInfo = new cSerieInfoDesign[FinalTable.Count];

                        //EXT[2].Add(SF.GetOutPut()[0][2]);
                        //EXT[3].Add(S.GetOutPut()[0][0]);

                        //for (int IdxCurve = 0; IdxCurve < FinalTable.Count; IdxCurve++)
                        //{
                        //    cSerieInfoDesign TmpSerieInfo = new cSerieInfoDesign();
                        //    TmpSerieInfo.color = Color.FromArgb(100, GlobalInfo.ListCellularPhenotypes[IdxCurve % GlobalInfo.ListCellularPhenotypes.Count].ColourForDisplay);

                        //    TmpSerieInfo.markerStyle = MarkerStyle.Circle;

                        //    VS1.Chart.ArraySeriesInfo[IdxCurve] = TmpSerieInfo;
                        //}

                        VS1.Run();

                        DS.SetInputData(VS1.GetOutPut());
                        DS.SetInputData(VT.GetOutPut());
                        DS.Orientation = Orientation.Horizontal;
                        DS.Title = "Noise Stdev " + NoiseLevel;
                        DS.Run();
                        DT.SetInputData(DS.GetOutPut());


                        //  EXT.ListRowNames.Add(DS.Title);

                    }

                    DT.Run();

                    //cDisplayToWindow DTW = new cDisplayToWindow();
                    //DTW.SetInputData(DT.GetOutPut());
                    //DTW.Run();
                    //DTW.Display();

                    //cDisplayExtendedTable DET = new cDisplayExtendedTable();
                    //DET.SetInputData(EXT);
                    //DET.DigitNumber = -1;
                    //DET.Run();  


                    FullResults.Add(ListPValues);
                }

            }

            cDisplayExtendedTable DET = new cDisplayExtendedTable();
            DET.SetInputData(FullResults);
            DET.DigitNumber = -1;
            DET.Run();

        }
コード例 #5
0
ファイル: WindowHCSAnalyzer.cs プロジェクト: cyrenaique/HCSA
        private void aNOVAToolStripMenuItem1_Click(object sender, EventArgs e)
        {
            cGUI_ListClasses GUI_ListClasses = new cGUI_ListClasses();
            GUI_ListClasses.IsCheckBoxes = true;
            GUI_ListClasses.IsSelectAll = true;


            if (GUI_ListClasses.Run().IsSucceed == false) return;
            cExtendedTable ListClassSelected = GUI_ListClasses.GetOutPut();

            string SubTitle = "ANOVA (One-Way)";


            #region single plate and plate by plate

            cDesignerTab DT = new cDesignerTab();
            if ((ProcessModeCurrentPlateOnlyToolStripMenuItem.Checked) || (ProcessModeplateByPlateToolStripMenuItem.Checked)/*||(ProcessModeEntireScreeningToolStripMenuItem.Checked)*/)
            {
                List<cPlate> ListPlatesToProcess = new List<cPlate>();
                if ((ProcessModeplateByPlateToolStripMenuItem.Checked)/*||(ProcessModeEntireScreeningToolStripMenuItem.Checked)*/)
                {
                    foreach (cPlate TmpPlate in cGlobalInfo.CurrentScreening.ListPlatesActive)
                        ListPlatesToProcess.Add(TmpPlate);
                }
                else
                    ListPlatesToProcess.Add(cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate());

                foreach (cPlate TmpPlate in ListPlatesToProcess)
                {
                    cExtendedTable NewTable1 = new cExtendedTable();
                    List<cListWells> ListListWells = new List<cListWells>();


                    int NumWells = 0;

                    for (int IdxClassWell = 0; IdxClassWell < ListClassSelected[0].Count; IdxClassWell++)
                    {
                        if (ListClassSelected[0][IdxClassWell] >= 1)
                        {
                            List<cWellClassType> LCT = new List<cWellClassType>();
                            LCT.Add(cGlobalInfo.ListWellClasses[IdxClassWell]);

                            cListWells TmpList = TmpPlate.ListWells.Filter(LCT);

                            if (TmpList.Count >= 3)
                            {
                                ListListWells.Add(TmpList);
                                NumWells += TmpList.Count;
                            }
                        }
                    }

                    if (ListListWells.Count <= 1)
                    {
                        if (ProcessModeCurrentPlateOnlyToolStripMenuItem.Checked)
                        {
                            MessageBox.Show("Insufficient number of control wells", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
                            return;
                        }
                        else
                            continue;
                    }


                    cExtendedTable CompleteReport = null;
                    cExtendedList ListZ = new cExtendedList();
                    List<cDescriptorType> ListDescForZFactor = new List<cDescriptorType>();
                    List<string> ListNames = new List<string>();
                    int RealIdx = 0;
                    for (int IDxDesc = 0; IDxDesc < cGlobalInfo.CurrentScreening.ListDescriptors.Count; IDxDesc++)
                    {
                        if (!cGlobalInfo.CurrentScreening.ListDescriptors[IDxDesc].IsActive()) continue;

                        cExtendedTable TableForZ = new cExtendedTable();

                        foreach (var item in ListListWells)
                        {
                            List<cDescriptorType> LType = new List<cDescriptorType>();
                            LType.Add(cGlobalInfo.CurrentScreening.ListDescriptors[IDxDesc]);
                            cExtendedTable TTable = item.GetAverageDescriptorValues(LType, false, false);
                            TableForZ.Add(TTable[0]);
                        }
                        RealIdx++;

                        cANOVA ZF = new cANOVA();
                        ZF.SetInputData(TableForZ);
                        ZF.Run();
                        ListZ.Add(ZF.GetOutPut()[0][0]);

                        ZF.GetOutPut()[0].Name = cGlobalInfo.CurrentScreening.ListDescriptors[IDxDesc].GetName();

                        if (CompleteReport == null)
                            CompleteReport = new cExtendedTable(ZF.GetOutPut());
                        else
                        {
                            cMerge M = new cMerge();
                            M.IsHorizontal = true;
                            M.SetInputData(CompleteReport, ZF.GetOutPut());
                            M.Run();
                            CompleteReport = M.GetOutPut();
                        }

                        ListDescForZFactor.Add(cGlobalInfo.CurrentScreening.ListDescriptors[IDxDesc]);
                    }

                    cExtendedTable ET = new cExtendedTable(new cExtendedTable(ListZ));
                    ET[0].ListTags = new List<object>();
                    ET[0].ListTags.AddRange(ListDescForZFactor);
                    ET.Name = TmpPlate.GetName() + "\n" + SubTitle + " - " + NumWells + " wells";// +" - " +cGlobalInfo.ListWellClasses[IdxClassNeg].Name + " (" + NewTable1[0].Count + " wells) vs. " +cGlobalInfo.ListWellClasses[IdxClassPos].Name + " (" + NewTable2[0].Count + " wells)";
                    ET[0].Name = ET.Name;

                    cSort S = new cSort();
                    S.SetInputData(ET);
                    S.IsAscending = false;
                    S.ColumnIndexForSorting = 0;
                    S.Run();

                    //ZFactorList.Sort(delegate(cSimpleSignature p1, cSimpleSignature p2) { return p1.AverageValue.CompareTo(p2.AverageValue); });

                    cViewerGraph1D VG1 = new cViewerGraph1D();
                    VG1.SetInputData(S.GetOutPut());

                    VG1.Chart.LabelAxisY = SubTitle;
                    VG1.Chart.LabelAxisX = "Descriptor";
                    VG1.Chart.IsZoomableX = true;
                    VG1.Chart.IsBar = true;
                    VG1.Chart.IsBorder = true;
                    VG1.Chart.IsDisplayValues = true;
                    VG1.Chart.IsShadow = true;
                    VG1.Chart.MarkerSize = 4;

                    //VG1.Chart.Max
                    VG1.Title = TmpPlate.GetName();

                    // Classes.Base_Classes.General.cLineHorizontalForGraph VLZ05 = new Classes.Base_Classes.General.cLineHorizontalForGraph(.05);
                    // VLZ05.IsAllowMoving = true;
                    //  VG1.Chart.ListHorizontalLines.Add(VLZ05);

                    VG1.Run();

                    cDesignerSplitter DS = new cDesignerSplitter();
                    DS.Orientation = Orientation.Vertical;
                    DS.SetInputData(VG1.GetOutPut());


                    cTranspose T = new cTranspose();
                    T.SetInputData(CompleteReport);
                    T.Run();
                    CompleteReport = T.GetOutPut();
                    CompleteReport[0].Name = "P-Value";
                    CompleteReport[1].Name = "Is significant ?";

                    cSort S1 = new cSort();
                    S1.SetInputData(CompleteReport);
                    S1.ColumnIndexForSorting = 0;
                    S1.IsAscending = true;
                    S1.Run();



                    cViewerTable VT = new cViewerTable();
                    VT.SetInputData(S1.GetOutPut());
                    VT.DigitNumber = -1;
                    VT.Run();

                    DS.SetInputData(VT.GetOutPut());
                    DS.Title = TmpPlate.GetName();
                    DS.Run();

                    DT.SetInputData(DS.GetOutPut());
                }
                DT.Run();

                cDisplayToWindow CDW = new cDisplayToWindow();
                CDW.SetInputData(DT.GetOutPut());//VG1.GetOutPut());


                if (ProcessModeCurrentPlateOnlyToolStripMenuItem.Checked)
                    CDW.Title = SubTitle + " - " + ListPlatesToProcess[0].GetName();
                else
                    CDW.Title = SubTitle + " - " + ListPlatesToProcess.Count + " plates";

                CDW.Run();
                CDW.Display();
            }
            #endregion

            #region entire screening
            else if (ProcessModeEntireScreeningToolStripMenuItem.Checked)
            {
                List<cPlate> ListPlatesToProcess = new List<cPlate>();
                foreach (cPlate TmpPlate in cGlobalInfo.CurrentScreening.ListPlatesActive)
                    ListPlatesToProcess.Add(TmpPlate);

                cExtendedList ListZ = new cExtendedList();
                List<cPlate> ListPlatesForZFactor = new List<cPlate>();
                foreach (cPlate TmpPlate in ListPlatesToProcess)
                {
                    cListWells ListWellsToProcess1 = new cListWells(null);
                    cListWells ListWellsToProcess2 = new cListWells(null);

                    foreach (cWell item in TmpPlate.ListActiveWells)
                    {
                        if (item.GetCurrentClassIdx() != -1)
                        {
                            if (ListClassSelected[0][item.GetCurrentClassIdx()] == 1)
                                ListWellsToProcess1.Add(item);
                            if (ListClassSelected[1][item.GetCurrentClassIdx()] == 1)
                                ListWellsToProcess2.Add(item);
                        }
                    }

                    cExtendedTable NewTable1 = new cExtendedTable(ListWellsToProcess1, cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorIndex(cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptor()));
                    cExtendedTable NewTable2 = new cExtendedTable(ListWellsToProcess2, cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorIndex(cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptor()));
                    //cExtendedTable NewTable2 = new cExtendedTable(ListWellsToProcess2, false);

                    if ((NewTable1.Count == 0) || (NewTable1[0].Count < 2) || (NewTable2.Count == 0) || (NewTable2[0].Count < 2))
                    {
                        if (ProcessModeCurrentPlateOnlyToolStripMenuItem.Checked)
                        {
                            MessageBox.Show("Insufficient number of control wells", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
                            return;
                        }
                        else
                            continue;
                    }

                    cExtendedTable TableForZ = new cExtendedTable();

                    TableForZ.Add(NewTable1[0]);
                    TableForZ.Add(NewTable2[0]);

                    cStudent_tTest ZF = new cStudent_tTest();
                    ZF.SetInputData(TableForZ);
                    ZF.Run();
                    double Zfactor = ZF.GetOutPut()[0][1];
                    ListZ.Add(Zfactor);

                    // update plate quality
                    //TmpPlate.ListProperties.UpdateValueByName("Quality", Math.Exp(Zfactor - 1));
                    //cProperty Prop = TmpPlate.ListProperties.FindByName("Quality");
                    //Prop.Info = ZF.GetInfo();

                    ListPlatesForZFactor.Add(TmpPlate);
                }


                cExtendedTable ET = new cExtendedTable(new cExtendedTable(ListZ));
                ET[0].ListTags = new List<object>();
                ET[0].ListTags.AddRange(ListPlatesForZFactor);
                ET.Name = SubTitle + " - " + cGlobalInfo.CurrentScreening.ListDescriptors[cGlobalInfo.CurrentScreening.ListDescriptors.CurrentSelectedDescriptorIdx].GetName();// +" - " +cGlobalInfo.ListWellClasses[IdxClassNeg].Name + /*" (" + NewTable1[0].Count + " wells)*/ " vs. " +cGlobalInfo.ListWellClasses[IdxClassPos].Name;// +" (" + NewTable2[0].Count + " wells)";
                ET[0].Name = ET.Name;

                cViewerGraph1D VG1 = new cViewerGraph1D();
                VG1.SetInputData(ET);

                VG1.Chart.LabelAxisY = SubTitle;
                VG1.Chart.LabelAxisX = "Plate";
                VG1.Chart.IsZoomableX = true;
                VG1.Chart.IsBar = true;
                VG1.Chart.IsBorder = true;
                VG1.Chart.IsDisplayValues = true;
                VG1.Chart.IsShadow = true;
                VG1.Chart.MarkerSize = 4;



                VG1.Title = cGlobalInfo.CurrentScreening.ListDescriptors[cGlobalInfo.CurrentScreening.ListDescriptors.CurrentSelectedDescriptorIdx].GetName();
                VG1.Run();

                cDisplayToWindow CDW = new cDisplayToWindow();
                CDW.SetInputData(VG1.GetOutPut());
                CDW.Title = SubTitle + " - " + ListPlatesToProcess.Count + " plates";
                CDW.Run();
                CDW.Display();
            #endregion
            }

        }
コード例 #6
0
ファイル: HCSAnalyzer2.cs プロジェクト: cyrenaique/HCSA
        /// <summary>
        /// This function displays the evolution of the average value of a certain descriptor through the plates, for a specified class
        /// </summary>
        /// <param name="sender"></param>
        /// <param name="e"></param>
        private void descriptorEvolutionToolStripMenuItem_Click(object sender, EventArgs e)
        {
            //  if (CompleteScreening == null) return;

            #region extract classes of interest
            cGUI_ListClasses GUI_ListClasses = new cGUI_ListClasses();
            GUI_ListClasses.IsCheckBoxes = !_DescEvolCellByCellItem.Checked;
            GUI_ListClasses.IsSelectAll = false;

            if (GUI_ListClasses.Run().IsSucceed == false) return;
            cExtendedTable ListClassSelected = GUI_ListClasses.GetOutPut();

            if (ListClassSelected.Sum() < 1)
            {
                MessageBox.Show("At least one classe has to be selected.", "Error !", MessageBoxButtons.OK, MessageBoxIcon.Error);
                return;
            }
            #endregion

            cDescriptorType DT = cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptor();

            cGUI_ListPlates GUI_ListPlates = new cGUI_ListPlates();
            GUI_ListPlates.IsCheckBoxes = true;
            GUI_ListPlates.ListInitialPlates = cGlobalInfo.CurrentScreening.ListPlatesActive;
            // GUI_ListClasses.ListInitialPlates = null;
            cFeedBackMessage FBM = GUI_ListPlates.Run();
            richTextBoxConsole.AppendText(FBM.Message);
            if (!FBM.IsSucceed) return;

            cListPlates LP = GUI_ListPlates.GetOutPut();

            if (_DescEvolCellByCellItem.Checked)
            {
                cExtendedTable FinalTable = new cExtendedTable();
                foreach (cPlate CurrentPlate in LP)
                {
                    cExtendedTable TmpFinalTable = new cExtendedTable();

                    int NumberOfWells = 0;
                    foreach (cWell item in CurrentPlate.ListActiveWells)
                    {
                        if (item.GetCurrentClassIdx() == -1) continue;
                        if (ListClassSelected[0][item.GetCurrentClassIdx()] == 1)
                        {
                            cExtendedTable TmpET = item.GetValuesList(DT);

                            if (TmpFinalTable.Count == 0)
                            {
                                TmpFinalTable = new cExtendedTable(TmpET);
                            }
                            else
                            {
                                cMerge M = new cMerge();
                                M.IsHorizontal = false;
                                M.SetInputData(TmpFinalTable, TmpET);
                                M.Run();
                                TmpFinalTable = M.GetOutPut();
                            }
                            NumberOfWells++;
                        }
                    }

                    if (NumberOfWells == 0) continue;

                    if (FinalTable.Count == 0)
                    {
                        FinalTable = new cExtendedTable(TmpFinalTable);
                        FinalTable[0].Name = CurrentPlate.GetName() + " (" + NumberOfWells + " wells)";
                    }
                    else
                    {
                        cMerge M = new cMerge();
                        M.IsHorizontal = true;
                        TmpFinalTable[0].Name = CurrentPlate.GetName() + " (" + NumberOfWells + " wells)";
                        M.SetInputData(FinalTable, TmpFinalTable);
                        M.Run();
                        FinalTable = M.GetOutPut();
                    }

                }
                cViewerHistogram VH = new cViewerHistogram();
                FinalTable.Name = DT.GetName();
                VH.Chart.LabelAxisX = DT.GetName();
                VH.Chart.IsArea = true;
                VH.Chart.IsPoint = false;
                //VH.Chart.IsBar = false;
                //VH.Chart.IsShadow = true;
                VH.Chart.IsXGrid = VH.Chart.IsYGrid = false;
                VH.Chart.Opacity = 200;
                VH.Chart.IsLegend = true;
                VH.SetInputData(FinalTable);
                VH.Chart.CurrentTitle.Text = cGlobalInfo.CurrentScreening.ListPlatesActive.Count + " plates";
                VH.Run();

                cDisplayToWindow DTW = new cDisplayToWindow();
                DTW.SetInputData(VH.GetOutPut());
                DTW.Title = "Cell-by-Cell Descriptor Evolution";
                DTW.Run();

                DTW.Display();

                //cExtendedTable ET = CompleteScreening.GetCurrentDisplayPlate().DBConnection.GetWellValues(
                //    this.AssociatedPlate.DBConnection.GetWellValues(this,
                //                         LCDT,
                //                         ListCellularPhenotypesToBeSelected);
            }
            else
            {
                cDisplayDescriptorEvolutions DEV = new cDisplayDescriptorEvolutions();
                DEV.ListPlates = LP;
                DEV.SetInputData(ListClassSelected);
                DEV.Run(cGlobalInfo.CurrentScreening);
            }
        }
コード例 #7
0
        public cFeedBackMessage Run(bool IsDisplayResults)
        {
            cMachineLearning MachineLearning = new cMachineLearning(/*cWell.GlobalInfo*/null);
            ParamAlgoForClustering = MachineLearning.AskAndGetClusteringAlgo();

            if (MinObjectsNumber == -1)
                MinObjectsNumber = (cGlobalInfo.CurrentScreening.Columns * cGlobalInfo.CurrentScreening.Rows * (int)cGlobalInfo.OptionsWindow.numericUpDownSystemMinWellRatio.Value) / 100;

            foreach (cPlate CurrentPlate in PlatesToProcess)
            {
                cExtendedTable CurrentPlateResult = null;

                foreach (var item in this.DescriptorsToProcess)
                {
                    cExtendedTable ET = CurrentPlate.GetAverageValueList(item, false);
                    ET.Name = item.GetName();

                    cExtendedTable ResultTable = this.GenerateArtifactMessage(ET, CurrentPlate);
                    ResultTable.ListRowNames = new List<string>();
                    ResultTable.ListRowNames.Add(item.GetName());

                    if (CurrentPlateResult == null) CurrentPlateResult = new cExtendedTable(ResultTable);
                    else
                    {
                        cMerge M = new cMerge();
                        M.IsHorizontal = false;
                        M.SetInputData(CurrentPlateResult, ResultTable);
                        M.Run();
                        CurrentPlateResult = M.GetOutPut();
                    }

                }
                CurrentPlateResult.Name = CurrentPlate.GetName();
                CurrentPlateResult.Tag = CurrentPlate;

                this.Output.Add(CurrentPlateResult);
            }

            this.Output.Name = "Systematic Errors (" + PlatesToProcess.Count + " plate(s))";

            if (IsDisplayResults)
            {
                cDisplayToWindow DTW = new cDisplayToWindow();

                cDesignerMultiChoices DMC = new cDesignerMultiChoices();

                foreach (var item in this.Output)
                {

                    cDesignerSplitter DS = new cDesignerSplitter();
                    DS.Orientation = System.Windows.Forms.Orientation.Horizontal;
                    DS.Title = item.Name;

                    cViewerTable VT = new cViewerTable();
                    VT.SetInputData(item);
                    VT.DigitNumber = 0;
                    VT.Run();
                    DS.SetInputData(VT.GetOutPut());

                    cViewerHeatMap VHM = new cViewerHeatMap();
                    VHM.SetInputData(item);
                    VHM.IsAutomatedMinMax = false;
                    VHM.Min = 0;
                    VHM.Max = 1;
                    VHM.Run();
                    DS.SetInputData(VHM.GetOutPut());

                    DS.Run();
                    cExtendedControl TmpXCtrl = DS.GetOutPut();
                    TmpXCtrl.Tag = item.Tag;
                    DMC.SetInputData(TmpXCtrl);

                }

                DMC.Run();
                DTW.SetInputData(DMC.GetOutPut());
                DTW.Title = "Systematic Errors [" + PlatesToProcess.Count + " plate(s)]";

                DTW.Run();
                DTW.Display();

                //cDisplayListExtendedTable DLET = new cDisplayListExtendedTable();
                //DLET.SetInputData(this.Output);
                //return DLET.Run();
            }

            return FeedBackMessage;
        }