public cFeedBackMessage Run()
{
if (this.Input == null)
{
FeedBackMessage.IsSucceed = false;
FeedBackMessage.Message = "No input data defined.";
return FeedBackMessage;
}
this.OutPut = new cListExtendedTable(this.Input);
return FeedBackMessage;
}
public cFeedBackMessage Run()
{
if (base.Start() == false)
{
base.FeedBackMessage.IsSucceed = false;
return base.FeedBackMessage;
}
#region parameters initilization
object _firstValue = base.ListProperties.FindByName("Kernel size");
int KernelSize = 0;
if (_firstValue == null)
{
base.GenerateError("Kernel size not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
KernelSize = (int)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("Kernel size cast didn't work");
return base.FeedBackMessage;
}
_firstValue = base.ListProperties.FindByName("Image width");
int ImWidth = 0;
if (_firstValue == null)
{
base.GenerateError("Image width not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
ImWidth = (int)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("Image width cast didn't work");
return base.FeedBackMessage;
}
_firstValue = base.ListProperties.FindByName("Image height");
int ImHeight = 0;
if (_firstValue == null)
{
base.GenerateError("Image height not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
ImHeight = (int)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("Image height cast didn't work");
return base.FeedBackMessage;
}
_firstValue = base.ListProperties.FindByName("Image depth");
int ImDepth = 0;
if (_firstValue == null)
{
base.GenerateError("Image depth not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
ImDepth = (int)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("Image depth cast didn't work");
return base.FeedBackMessage;
}
#endregion
if (this.Input[0].Count == 2) ImDepth = 1;
if (this.Input[0].Count == 1)
{
ImDepth = 1;
ImHeight = 1;
}
this.Output = new cImage(ImWidth, ImHeight, ImDepth, this.Input.Count);
cImageDrawKernel GK = new cImageDrawKernel();
GK.sigma_x = KernelSize;
GK.sigma_y = KernelSize;
GK.sigma_z = KernelSize;
GK.Run();
cImage K = GK.GetOutPut();
for (int IdxChannel = 0; IdxChannel < this.Input.Count; IdxChannel++)
{
cExtendedTable CurrentTable = this.Input[IdxChannel];
cExtendedList ListVolumes = new cExtendedList();
double MaxX = CurrentTable[0].Max();
double MinX = CurrentTable[0].Min();
double MaxY = CurrentTable[1].Max();
double MinY = CurrentTable[1].Min();
double MaxZ = 0;
double MinZ = 0;
if (CurrentTable.Count>2)
{
MaxZ = CurrentTable[2].Max();
MinZ = CurrentTable[2].Min();
}
this.Output.SingleChannelImage[IdxChannel].Resolution.X = (MaxX - MinX) / (double)ImWidth;
this.Output.SingleChannelImage[IdxChannel].Resolution.Y = (MaxY - MinY) / (double)ImHeight;
this.Output.SingleChannelImage[IdxChannel].Resolution.Z = (MaxZ - MinZ) / (double)ImDepth;
if (CurrentTable.Count > 2)
{
for (int j = 0; j < CurrentTable[0].Count; j++)
{
double TmpValueX = (ImWidth * (CurrentTable[0][j] - MinX)) / (MaxX - MinX) - K.Width / 2;
double TmpValueY = (ImHeight * (CurrentTable[1][j] - MinY)) / (MaxY - MinY) - K.Height / 2;
double TmpValueZ = (ImDepth * (CurrentTable[2][j] - MinZ)) / (MaxZ - MinZ) - K.Depth / 2;
this.Output.AddInto(K, (int)TmpValueX, (int)TmpValueY, (int)TmpValueZ, IdxChannel);
}
}
else
{
for (int j = 0; j < CurrentTable[0].Count; j++)
{
double TmpValueX = (ImWidth * (CurrentTable[0][j] - MinX)) / (MaxX - MinX) - K.Width / 2;
double TmpValueY = ImHeight - (ImHeight * (CurrentTable[1][j] - MinY)) / (MaxY - MinY) - K.Height / 2;
this.Output.AddInto(K, (int)TmpValueX, (int)TmpValueY, 0, IdxChannel);
}
}
cListExtendedTable TablesForDensity = new cListExtendedTable(this.Output);
for (int idxChannel = 0; idxChannel < this.Output.GetNumChannels(); idxChannel++)
{
this.Output.SingleChannelImage[idxChannel].Name = this.Input.Name;//cGlobalInfo.ListCellularPhenotypes[idxChannel].Name;
float Sum = 1;
if (IsNormalized)
{
Sum = (float)TablesForDensity[idxChannel].Sum();
if (Sum <= 0.0) continue;
for (int i = 0; i < this.Output.SingleChannelImage[idxChannel].Data.Length; i++)
{
this.Output.SingleChannelImage[idxChannel].Data[i] = (10000000 * this.Output.SingleChannelImage[idxChannel].Data[i]) / Sum;
}
}
//else
//{
// for (int i = 0; i < this.Output.SingleChannelImage[idxChannel].Data.Length; i++)
// {
// // if (ClassPopulations[idxChannel] > 0)
// this.Output.SingleChannelImage[idxChannel].Data[i] = this.Output.SingleChannelImage[idxChannel].Data[i];
// }
//}
}
}
this.Output.SingleChannelImage[0].UpDateMax();
this.Output.SingleChannelImage[0].UpDateMin();
base.End();
return FeedBackMessage;
}
public void SetInputData(cListExtendedTable Input)
{
this.Input = Input;
}
private void dRC3DToolStripMenuItem_Click(object sender, EventArgs e)
{
if (cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptors().Count < 3)
{
MessageBox.Show("At least 3 descriptors are required for this operation !", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
cListExtendedTable LET = new cListExtendedTable();
//List<cListWells> ListWells = new List<cListWells>();
//ListWells.Add(cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().ListActiveWells);
// firstly, wells are grouped by class
//foreach (var item in cGlobalInfo.ListWellClasses)
//{
// List<cWellClassType> TypeForFilter = new List<cWellClassType>();
// TypeForFilter.Add(item);
// cListWells TmpListWells = cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().ListActiveWells.Filter(TypeForFilter);
// cGeneralDRC gDRC = new cGeneralDRC(TmpListWells);
// LET.Add(gDRC.ListAverageValues);
//}
for (int i = 0; i < 3; i++)
{
List<int> GroupForFilter = new List<int>();
GroupForFilter.Add(i);
cListWells TmpListWells = cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().ListActiveWells.FilterByGroup(GroupForFilter);
cGeneralDRC gDRC = new cGeneralDRC(TmpListWells);
LET.Add(gDRC.ListAverageValues);
}
cViewer3D V3D = new cViewer3D();
c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));
c3DObjectScatterPoints _3DScatterPt = new c3DObjectScatterPoints();
//_3DScatterPt.SetInputData(cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().ListActiveWells.GetDescriptorValues(cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptors(), false));
// _3DScatterPt.GlobalInfo = this.GlobalInfo;
_3DScatterPt.SetInputData(LET);
// _3DScatterPt.IsLinked = true;
_3DScatterPt.Run(MyWorld);
cListGeometric3DObject GlobalList = _3DScatterPt.GetOutPut();
foreach (var item in GlobalList)
{
MyWorld.AddGeometric3DObject(item);
}
MyWorld.BackGroundColor = cGlobalInfo.OptionsWindow.FFAllOptions.panelFor3DBackColor.BackColor;
V3D.SetInputData(MyWorld);
V3D.Run();
cDisplayToWindow DTW = new cDisplayToWindow();
DTW.SetInputData(V3D.GetOutPut());
DTW.Title = "3D Dose Response Visualization";
DTW.Run();
DTW.Display();
}
public void Run()
{
// define names
string[] VarNames = new string[Input.Count];
double[][] dataset = new double[Input.Count][];
int Idx = 0;
foreach (var item in Input)
{
dataset[Idx] = new double[item.Count];
Array.Copy(item.ToArray(), dataset[Idx], item.Count);
VarNames[Idx++] = item.Name;
}
//// define data
data.Dataset data_Set = new data.Dataset(dataset, VarNames, 0);
analysis.VarPairQueue Qu = new analysis.VarPairQueue(data_Set);
for(int Idx_0=0;Idx_0<this.Input.Count;Idx_0++)
for (int Idx_1 = 0; Idx_1 <= Idx_0; Idx_1++)
Qu.addPair(Idx_1,Idx_0);
Analysis ana = new Analysis(data_Set, Qu);
AnalysisParameters param = new AnalysisParameters();
double resparam = param.commonValsThreshold;
java.lang.Class t = java.lang.Class.forName("analysis.results.FullResult");
if(this.Is_BriefReport)
t = java.lang.Class.forName("analysis.results.BriefResult");
ana.analyzePairs(t, param);
analysis.results.Result[] res = ana.getSortedResults();
List<string[]> ListValues = new List<string[]>();
List<bool> ListIscolor = new List<bool>();
for (Idx = 0; Idx < res.Length; Idx++)
{
ListValues.Add(res[Idx].toString().Split(','));
}
string[] ListNames = res[0].getHeader().Split(',');
this.Output = new cListExtendedTable();
for (int IdxTest = 2; IdxTest < ListNames.Length; IdxTest++) // loop over all the different type of results
{
// remove useless informations
if (ListNames[IdxTest] == "MI via KDE") continue;
if (ListNames[IdxTest] == "Fisher") continue;
if (ListNames[IdxTest] == "last value") continue;
if (ListNames[IdxTest] == "MAS found at (X)") continue;
if (ListNames[IdxTest] == "MAS found at (Y)") continue;
if (ListNames[IdxTest] == "MICfound at (Y)") continue;
double[,] TmpTable = new double[VarNames.Length, VarNames.Length];
for (int i = 0; i < res.Length; i++) // loop over the different pairs
{
string TmpName0 = res[i].getXVar();
string TmpName1 = res[i].getYVar();
int Idx_var0 = 0;
int Idx_var1 = 0;
for (Idx_var0 = 0; Idx_var0 < VarNames.Length; Idx_var0++)
if(VarNames[Idx_var0]==TmpName0)
break;
for (Idx_var1 = 0; Idx_var1 < VarNames.Length; Idx_var1++)
if (VarNames[Idx_var1] == TmpName1)
break;
double Value=0;
double.TryParse(res[i].toString().Split(',')[IdxTest], out Value);
TmpTable[Idx_var0, Idx_var1] = TmpTable[Idx_var1, Idx_var0] = Value;
}
cExtendedTable NewTable = new cExtendedTable(TmpTable);
NewTable.ListRowNames = new List<string>();
for (int i = 0; i < VarNames.Length; i++)
{
NewTable.ListRowNames.Add(VarNames[i]);
NewTable[i].Name = VarNames[i];
if (CurrentScreening != null)
{
int IdxDesc = cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorIndex(NewTable[i].Name);
if (IdxDesc > -1)
{
NewTable[i].Tag = cGlobalInfo.CurrentScreening.ListDescriptors[IdxDesc];
}
}
}
NewTable.Name = ListNames[IdxTest];
this.Output.Add(NewTable);
}
}
public void SetInputData(cListExtendedTable ListInput)
{
//CurrentPanelHisto = new cPanelHisto(ListValues, true, eGraphType.LINE, this.Orientation);
// Chart = new cChart1DGraph();
Chart.ListInput = ListInput;
}
private void ToolStripMenuItem_DisplayHistograms(object sender, EventArgs e)
{
cDesignerTab DT = new cDesignerTab();
cListExtendedTable ListTables = new cListExtendedTable(this.AssociatedImage);
for (int i = 0; i < ListTables.Count; i++)
{
cLinearize LI = new cLinearize();
LI.SetInputData(ListTables[i]);
LI.Run();
cViewerStackedHistogram VH = new cViewerStackedHistogram();
VH.SetInputData(LI.GetOutPut());
VH.Title = ListTables[i].Name;
if (!VH.Run().IsSucceed) return;
DT.SetInputData(VH.GetOutPut());
}
DT.Run();
cDisplayToWindow MyDisplay = new cDisplayToWindow();
MyDisplay.SetInputData(DT.GetOutPut());
MyDisplay.Title = "Histograms(" + this.AssociatedImage.Name + ")";
MyDisplay.Run();
MyDisplay.Display();
}
public void PerformClassification()
{
FormForSingleCellClassifOptions FFSC = new FormForSingleCellClassifOptions();
//cGUI_ListClasses GLC = new cGUI_ListClasses();
//GLC.ClassType = eClassType.PHENOTYPE;
//GLC.IsCheckBoxes = true;
//GLC.IsSelectAll = true;
//GLC.Run(GlobalInfo);
PanelForClassSelection PhenotypeSelectionPanel = new PanelForClassSelection( true, eClassType.PHENOTYPE);
PhenotypeSelectionPanel.Height = FFSC.panelPhenoToBeClassified.Height;
FFSC.panelPhenoToBeClassified.Controls.Add(PhenotypeSelectionPanel);
PanelForClassSelection WellClassSelectionPanel = new PanelForClassSelection( true, eClassType.WELL);
WellClassSelectionPanel.Height = FFSC.panelWellToBeClassified.Height;
FFSC.panelWellToBeClassified.Controls.Add(WellClassSelectionPanel);
PanelForPlatesSelection PlatesSelectionPanel = new PanelForPlatesSelection( true, null, true);
PlatesSelectionPanel.Height = FFSC.panelWellToBeClassified.Height;
FFSC.tabPagePlates.Controls.Add(PlatesSelectionPanel);
if (FFSC.ShowDialog() != DialogResult.OK) return;
// ----------------------- Classification ------------------------------
int DescrCount = cGlobalInfo.CurrentScreening.ListDescriptors.Count;
this.UpDateNumberOfCluster();
if (NumberOfClusters == 0)
{
System.Windows.Forms.MessageBox.Show("Number of cluster is null", "Error !", MessageBoxButtons.OK, MessageBoxIcon.Hand);
return;
}
//if (FFSC.checkBoxGenerationRatio.Checked)
//{
// // first we update the descriptor
// for (int i = 0; i < this.NumberOfClusters; i++)
// GlobalInfo.CurrentScreening.ListDescriptors.AddNew(new cDescriptorType("Ratio_" + GlobalInfo.ListCellularPhenotypes[i].Name, true, 1, GlobalInfo));
//}
FormForProgress ProgressWindow = new FormForProgress();
ProgressWindow.Show();
int IdxProgress = 0;
int MaxProgress = 0;
#region Confusion Matrix init
cListExtendedTable LT = new cListExtendedTable();
cExtendedTable ConfusionMatrix = new cExtendedTable(cGlobalInfo.ListCellularPhenotypes.Count, cGlobalInfo.ListCellularPhenotypes.Count, 0);
ConfusionMatrix.Name = "Confusion Matrix (global)";
ConfusionMatrix.ListRowNames = new List<string>();
for (int i = 0; i < cGlobalInfo.ListCellularPhenotypes.Count; i++)
{
ConfusionMatrix.ListRowNames.Add(cGlobalInfo.ListCellularPhenotypes[i].Name + "*");
ConfusionMatrix[i].Name = cGlobalInfo.ListCellularPhenotypes[i].Name;
}
LT.Add(ConfusionMatrix);
for (int i = 0; i < cGlobalInfo.ListWellClasses.Count; i++)
{
cExtendedTable ConfusionMatrixTmp = new cExtendedTable(cGlobalInfo.ListCellularPhenotypes.Count, cGlobalInfo.ListCellularPhenotypes.Count, 0);
ConfusionMatrixTmp.Name = "Confusion Matrix - " + cGlobalInfo.ListWellClasses[i].Name;
ConfusionMatrixTmp.ListRowNames = new List<string>();
for (int j = 0; j < cGlobalInfo.ListCellularPhenotypes.Count; j++)
{
ConfusionMatrixTmp.ListRowNames.Add(cGlobalInfo.ListCellularPhenotypes[j].Name + "*");
ConfusionMatrixTmp[j].Name =cGlobalInfo.ListCellularPhenotypes[j].Name;
}
LT.Add(ConfusionMatrixTmp);
}
#endregion
cListPlates LP = PlatesSelectionPanel.GetListSelectedPlates();
foreach (cPlate CurrentPlateToProcess in LP /*GlobalInfo.CurrentScreening.ListPlatesAvailable*/)
MaxProgress += (int)CurrentPlateToProcess.ListActiveWells.Count;
ProgressWindow.progressBar.Maximum = MaxProgress;
FastVector attVals = new FastVector();
for (int i = 0; i < this.NumberOfClusters; i++)
attVals.addElement(i.ToString());
cPlate CurrentDispPlate = cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate();
foreach (cPlate CurrentPlateToProcess in LP/* GlobalInfo.CurrentScreening.ListPlatesAvailable*/)
{
foreach (cWell TmpWell in CurrentPlateToProcess.ListActiveWells)
{
ProgressWindow.progressBar.Value = IdxProgress++;
if (TmpWell.GetCurrentClassIdx() == -1) continue;
if (WellClassSelectionPanel.ListCheckBoxes[TmpWell.GetCurrentClassIdx()].Checked == false) continue;
DataTable FinalDataTable = new DataTable();
TmpWell.AssociatedPlate.DBConnection = new cDBConnection(TmpWell.AssociatedPlate, TmpWell.SQLTableName);
TmpWell.AssociatedPlate.DBConnection.AddWellToDataTable(TmpWell, FinalDataTable, this.GlobalInfo);
cListSingleBiologicalObjects LSBO = TmpWell.AssociatedPlate.DBConnection.GetBiologicalPhenotypes(TmpWell);
//TmpWell.AssociatedPlate.DBConnection.AddWellToDataTable(TmpWell, FinalDataTable, checkBoxIncludeWellClassAsDesc.Checked, GlobalInfo);
Instances ListInstancesTOClassify = this.CreateInstancesWithoutClass(FinalDataTable);
ListInstancesTOClassify.insertAttributeAt(new weka.core.Attribute("Class", attVals), ListInstancesTOClassify.numAttributes());
ListInstancesTOClassify.setClassIndex(ListInstancesTOClassify.numAttributes() - 1);
cExtendedList ListNewClasses = new cExtendedList();
int NumInstances = ListInstancesTOClassify.numInstances();
for (int i = 0; i < NumInstances; i++)
{
// ClassId contains the new class
Instance CurrentInst = ListInstancesTOClassify.instance(i);
double classId = this.CurrentClassifier.classifyInstance(CurrentInst);
double[] ClassConfidence = this.CurrentClassifier.distributionForInstance(CurrentInst);
LSBO[i].ClassificationConfidence = ClassConfidence[(int)classId];
ListNewClasses.Add(classId);
if (CurrentPlateToProcess == CurrentDispPlate)
{
LT[0][LSBO[i].GetAssociatedPhenotype().Idx][(int)classId]++;
if (TmpWell.GetCurrentClassIdx() >= 0)
LT[TmpWell.GetCurrentClassIdx() + 1][LSBO[i].GetAssociatedPhenotype().Idx][(int)classId]++;
}
}
ProgressWindow.richTextBoxForComment.AppendText(TmpWell.GetShortInfo().Remove(TmpWell.GetShortInfo().Length - 2) + " : " + NumInstances + " objects\n");
ProgressWindow.Refresh();
// ------------- update class within the database -----------------------------
TmpWell.AssociatedPlate.DBConnection.ChangePhenotypeClass(TmpWell, ListNewClasses);
//if (FFSC.checkBoxGenerationRatio.Checked)
//{
// List<double[]> Histo = ListNewClasses.CreateHistogram(0, ListInstancesTOClassify.numClasses(), ListInstancesTOClassify.numClasses());
// cListSignature LDesc = new cListSignature();
// for (int IdxHisto = 0; IdxHisto < Histo[1].Length - 1; IdxHisto++)
// {
// Histo[1][IdxHisto] = (100.0 * Histo[1][IdxHisto]) / (double)ListInstancesTOClassify.numInstances();
// cSignature NewDesc = new cSignature(Histo[1][IdxHisto], GlobalInfo.CurrentScreening.ListDescriptors[IdxHisto + DescrCount], GlobalInfo.CurrentScreening);
// LDesc.Add(NewDesc);
// }
// TmpWell.AddSignatures(LDesc);
//}
TmpWell.AssociatedPlate.DBConnection.CloseConnection();
}
}
#region Display Report
cDesignerSplitter DS = new cDesignerSplitter();
DS.Orientation = Orientation.Vertical;
cViewertext VTEXT = new cViewertext();
VTEXT.SetInputData(ProgressWindow.richTextBoxForComment.Text);
VTEXT.Run();
cDesignerTab DT = new cDesignerTab();
DT.IsMultiline = false;
foreach (var item in LT)
{
cViewerTable VT = new cViewerTable();
VT.SetInputData(item);
VT.DigitNumber = 0;
VT.Run();
DT.SetInputData(VT.GetOutPut());
}
DT.Run();
cExtendedControl TextEC = DT.GetOutPut();
TextEC.Width = 0;
TextEC.Height = 0;
TextEC.Anchor = (System.Windows.Forms.AnchorStyles)(System.Windows.Forms.AnchorStyles.Top | System.Windows.Forms.AnchorStyles.Bottom
| System.Windows.Forms.AnchorStyles.Left
| System.Windows.Forms.AnchorStyles.Right);
DS.SetInputData(VTEXT.GetOutPut());
DS.SetInputData(TextEC);
DS.Run();
ProgressWindow.Close();
cDisplayToWindow CDT = new cDisplayToWindow();
CDT.SetInputData(DS.GetOutPut());
CDT.IsModal = true;
CDT.Title = "Phenotypic Classificaton Report";
CDT.Run();
CDT.Display();
#endregion
//if (IsKeepOriginalDesc == System.Windows.Forms.DialogResult.No)
//{
// // int DescNumToRemove = GlobalInfo.CurrentScreen.ListDescriptors.Count -
// for (int IdxDesc = 0; IdxDesc < DescrCount; IdxDesc++)
// GlobalInfo.CurrentScreening.ListDescriptors.RemoveDesc(GlobalInfo.CurrentScreening.ListDescriptors[0], GlobalInfo.CurrentScreening);
//}
cGlobalInfo.CurrentScreening.ListDescriptors.UpDateDisplay();
cGlobalInfo.CurrentScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; idxP++)
cGlobalInfo.CurrentScreening.ListPlatesActive[idxP].UpDataMinMax();
//WindowFormForCellbyCellClassif.Close();
//WindowClusteringInfo.Close();
}
public cFeedBackMessage Run()
{
if (base.Start() == false)
{
base.FeedBackMessage.IsSucceed = false;
return base.FeedBackMessage;
}
if ((this.Input == null)||(this.Input.Count==0))
{
FeedBackMessage.IsSucceed = false;
FeedBackMessage.Message = "No input data defined.";
return FeedBackMessage;
}
FeedBackMessage.IsSucceed = true;
#region Properties Management
object _firstValue = base.ListProperties.FindByName("Normalized ?");
bool IsNormalized = false;
if (_firstValue == null)
{
base.GenerateError("-Normalized ?- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
IsNormalized = (bool)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Normalized ?- cast didn't work");
return base.FeedBackMessage;
}
_firstValue = base.ListProperties.FindByName("Draw Axis ?");
bool IsdrawAxis = true;
if (_firstValue == null)
{
base.GenerateError("-Draw Axis ?- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
IsdrawAxis = (bool)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Draw Axis ?- cast didn't work");
return base.FeedBackMessage;
}
_firstValue = base.ListProperties.FindByName("Link Points ?");
bool IsLinked = false;
if (_firstValue == null)
{
base.GenerateError("-Link Points ?- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
IsLinked = (bool)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Link Points ?- cast didn't work");
return base.FeedBackMessage;
}
_firstValue = base.ListProperties.FindByName("Desc. 1");
string Desc1;
if (_firstValue == null)
{
base.GenerateError("-Desc. 1- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
Desc1 = (string)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Desc. 1- cast didn't work");
return base.FeedBackMessage;
}
cDescriptorType DescX = cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorByName(Desc1);
if (DescX == null)
{
base.GenerateError(Desc1 + " is not a descriptor !");
return base.FeedBackMessage;
}
_firstValue = base.ListProperties.FindByName("Desc. 2");
if (_firstValue == null)
{
base.GenerateError("-Desc. 2- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
Desc1 = (string)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Desc. 2- cast didn't work");
return base.FeedBackMessage;
}
cDescriptorType DescY = cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorByName(Desc1);
if (DescY == null)
{
base.GenerateError(Desc1 + " is not a descriptor !");
return base.FeedBackMessage;
}
_firstValue = base.ListProperties.FindByName("Desc. 3");
if (_firstValue == null)
{
base.GenerateError("-Desc. 3- not found !");
return base.FeedBackMessage;
}
try
{
cProperty TmpProp = (cProperty)_firstValue;
Desc1 = (string)TmpProp.GetValue();
}
catch (Exception)
{
base.GenerateError("-Desc. 2- cast didn't work");
return base.FeedBackMessage;
}
cDescriptorType DescZ = cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorByName(Desc1);
if (DescZ == null)
{
base.GenerateError(Desc1 + " is not a descriptor !");
return base.FeedBackMessage;
}
#endregion
List<cDescriptorType> ListDesc = new List<cDescriptorType>();
ListDesc.Add(DescX);
ListDesc.Add(DescY);
ListDesc.Add(DescZ);
cListExtendedTable LET = new cListExtendedTable();
foreach (var item in cGlobalInfo.ListWellClasses)
{
List<cWellClassType> TypeForFilter = new List<cWellClassType>();
TypeForFilter.Add(item);
cExtendedTable TmpTable = ((cListWells)this.Input.Filter(TypeForFilter)).GetAverageDescriptorValues(ListDesc,false, false);
if (TmpTable != null)
LET.Add(TmpTable);
}
cViewer3D V3D = new cViewer3D();
c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));
c3DObjectScatterPoints _3DScatterPt = new c3DObjectScatterPoints();
_3DScatterPt.ListProperties.FindByName("Draw Axis ?").SetNewValue(IsdrawAxis);
_3DScatterPt.ListProperties.FindByName("Normalized ?").SetNewValue(IsNormalized);
_3DScatterPt.ListProperties.FindByName("Link Points ?").SetNewValue(IsLinked);
_3DScatterPt.SetInputData(LET);
if (_3DScatterPt.Run(MyWorld).IsSucceed == false) return base.FeedBackMessage;
cListGeometric3DObject GlobalList = _3DScatterPt.GetOutPut();
foreach (var item in GlobalList)
{
MyWorld.AddGeometric3DObject(item);
}
MyWorld.BackGroundColor = cGlobalInfo.OptionsWindow.FFAllOptions.panelFor3DBackColor.BackColor;
V3D.SetInputData(MyWorld);
V3D.Run();
cDisplayToWindow DTW = new cDisplayToWindow();
DTW.SetInputData(V3D.GetOutPut());
DTW.Title = "3D Scatter Plot(List "+this.Input.Count +" Wells)";
DTW.Run();
DTW.Display();
return base.FeedBackMessage;
}
private void ToolStripMenuItem_Display3DScatterGraph(object sender, EventArgs e)
{
cExtendedTable CET = new cExtendedTable();
foreach (DataGridViewColumn item in GridView.SelectedColumns)
{
CET.Add(Input[item.Index]);
}
if (this.Input.ListTags != null)
{
CET.ListTags = new List<object>();
foreach (var item in this.Input.ListTags)
{
CET.ListTags.Add(item);
}
}
cListExtendedTable LET = new cListExtendedTable();
LET.Add(CET);
//List<cListWells> ListWells = new List<cListWells>();
//ListWells.Add(cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().ListActiveWells);
cViewer3D V3D = new cViewer3D();
c3DNewWorld MyWorld = new c3DNewWorld(new cPoint3D(1, 1, 1), new cPoint3D(1, 1, 1));
c3DObjectScatterPoints _3DScatterPt = new c3DObjectScatterPoints();
_3DScatterPt.ListProperties.FindByName("Draw Axis ?").SetNewValue((bool)true);
_3DScatterPt.ListProperties.FindByName("Draw Axis ?").IsGUIforValue = true;
_3DScatterPt.ListProperties.FindByName("Normalized ?").SetNewValue((bool)true);
_3DScatterPt.ListProperties.FindByName("Normalized ?").IsGUIforValue = true;
_3DScatterPt.ListProperties.FindByName("Link Points ?").SetNewValue((bool)false);
_3DScatterPt.ListProperties.FindByName("Link Points ?").IsGUIforValue = true;
//_3DScatterPt.GlobalInfo = cGlobalInfo;
_3DScatterPt.SetInputData(LET);
if (_3DScatterPt.Run(MyWorld).IsSucceed == false) return;
cListGeometric3DObject GlobalList = _3DScatterPt.GetOutPut();
foreach (var item in GlobalList)
{
MyWorld.AddGeometric3DObject(item);
}
V3D.SetInputData(MyWorld);
V3D.Run();
cDisplayToWindow DTW = new cDisplayToWindow();
DTW.SetInputData(V3D.GetOutPut());
DTW.Title = "3D Scatter Graph ("+ this.Input.Name +")";
DTW.Run();
DTW.Display();
}
public cFeedBackMessage Run(cScreening CompleteScreening)
{
if (this.Input == null)
{
FeedBackMessage.IsSucceed = false;
FeedBackMessage.Message = "No input data defined.";
return FeedBackMessage;
}
bool IsCurrentDescOnly = false;
if (this.ListPlates == null)
ListPlates = CompleteScreening.ListPlatesActive;
cDisplayToWindow CDW1 = new cDisplayToWindow();
cDesignerTab DT = new cDesignerTab();
foreach (cDescriptorType CurrentDesc in CompleteScreening.ListDescriptors.GetActiveDescriptors())
{
cListExtendedTable CompleteListOfData = new cListExtendedTable();
cExtendedTable FullTableAverage = new cExtendedTable();
FullTableAverage.ListRowNames = new List<string>();
string TableName = CurrentDesc.GetName() + " evolution\n" + Input[0].Sum() + " classes - ";
for (int i = 0; i < Input[0].Count; i++)
{
if ((Input[0][i] == 1) && (Input[0].ListTags != null) && (Input[0].ListTags[i].GetType() == typeof(cWellClassType)))
{
cWellClassType TmpWellClass = (cWellClassType)Input[0].ListTags[i];
CompleteListOfData.Add(new cExtendedTable());
CompleteListOfData[CompleteListOfData.Count - 1].Name = TmpWellClass.Name;
CompleteListOfData[CompleteListOfData.Count - 1].Tag = Input[0].ListTags[i];
FullTableAverage.Add(new cExtendedList(TmpWellClass.Name));
FullTableAverage[FullTableAverage.Count - 1].ListTags = new List<object>();
FullTableAverage[FullTableAverage.Count - 1].Name = TmpWellClass.Name;
FullTableAverage[FullTableAverage.Count - 1].Tag = TmpWellClass;
int IdxPlate = 0;
foreach (cPlate TmpPlate in CompleteScreening.ListPlatesActive)
{
FullTableAverage[FullTableAverage.Count - 1].Add(0);
FullTableAverage[FullTableAverage.Count - 1].ListTags.Add(TmpWellClass);
CompleteListOfData[CompleteListOfData.Count - 1].Add(new cExtendedList(TmpPlate.GetName()));
CompleteListOfData[CompleteListOfData.Count - 1][CompleteListOfData[CompleteListOfData.Count - 1].Count - 1].Tag = TmpPlate;
CompleteListOfData[CompleteListOfData.Count - 1][CompleteListOfData[CompleteListOfData.Count - 1].Count - 1].Add(IdxPlate);
IdxPlate++;
}
}
}
TableName += FullTableAverage[0].Count + " plates";
FullTableAverage.Name = TableName;
foreach (cPlate TmpPlate in CompleteScreening.ListPlatesActive)
FullTableAverage.ListRowNames.Add(TmpPlate.GetName());
// cDescriptorsType CurrentDesc = CompleteScreening.ListDescriptors.GetActiveDescriptor();
int RealIdx = 0;
for (int i = 0; i < Input[0].Count; i++)
{
if (Input[0][i] == 1)
{
int IdxPlate = 0;
foreach (cPlate TmpPlate in ListPlates/*CompleteScreening.ListPlatesActive*/)
{
cExtendedList CurrentListValues = new cExtendedList();
foreach (cWell item in TmpPlate.ListActiveWells)
if ((item.GetCurrentClassIdx() != -1) && (item.GetCurrentClassIdx() == i))
{
double Value = item.ListSignatures.GetSignature(CurrentDesc).GetValue();
CurrentListValues.Add(Value);
CompleteListOfData[RealIdx][IdxPlate].Add(Value);
}
FullTableAverage[RealIdx][IdxPlate] = CurrentListValues.Mean();
IdxPlate++;
}
RealIdx++;
}
}
cViewerGraph1D VG = new cViewerGraph1D();
VG.Chart.IsLine = true;
VG.Chart.IsShadow = true;
VG.Chart.IsZoomableX = true;
// VG.Chart.IsYGrid = true;
//VG.Chart.IsDisplayValues = true;
VG.Chart.IsLegend = true;
//cViewerStackedHistogram CV1 = new cViewerStackedHistogram();
// CV1.SetInputData(NewTable);
VG.SetInputData(FullTableAverage);
VG.SetInputData(CompleteListOfData);
VG.Chart.LabelAxisX = "Plate";
VG.Chart.LabelAxisY = CurrentDesc.GetName();
VG.Run();
cExtendedControl TmpCtrl = VG.GetOutPut();
TmpCtrl.Title = CurrentDesc.GetName();
DT.SetInputData(TmpCtrl);
}
DT.Run();
CDW1.Title = "Descriptor Evolution";
CDW1.SetInputData(DT.GetOutPut());
CDW1.Run();
CDW1.Display();
return FeedBackMessage;
}
void BuildFromListTable(cListExtendedTable ListSources)
{
if (ListSources.Count == 0) return;
if (ListSources[0].Count == 0) return;
if (ListSources[0][0].Count == 0) return;
//this.NumChannels = ListSources.Count;
this.Width = ListSources[0].Count;
this.Height = ListSources[0][0].Count;
this.Depth = 1;
this.SliceSize = this.Height * this.Width;
this.SingleChannelImage = new cListSingleChannelImage();
for (int IdxChannel = 0; IdxChannel < ListSources.Count; IdxChannel++)
{
this.SingleChannelImage.Add(new cSingleChannelImage(this.Width, this.Height, 1, new cPoint3D(1, 1, 1)));
for (int i = 0; i < this.Width; i++)
for (int j = 0; j < this.Height; j++)
{
this.SingleChannelImage[IdxChannel].Data[i + j * this.Width] = (float)ListSources[IdxChannel][i][j];
}
}
this.Name = ListSources.Name;
}
public cImage(cListExtendedTable ListSources)
{
this.BuildFromListTable(ListSources);
}
public void SetInputData(cListExtendedTable Input)
{
base.Title += ": " + Input.Name;
this.Input = Input;
}
public void SetInputData(cExtendedTable Input)
{
this.Input = new cListExtendedTable(Input);
}
private void buttonProcess_Click(object sender, EventArgs e)
{
ImageWidth = (int)numericUpDownMapWidth.Value;
ImageHeight = (int)numericUpDownMapHeight.Value;
if (this.radioButton2D.Checked) ImageDepth = 1;
else
ImageDepth = (int)numericUpDownMapDepth.Value;
//GlobalInfo.ListCellularPhenotypes[(int)MachineLearning.Classes[j]]
cImageDrawKernel GK = new cImageDrawKernel();
GK.sigma_x = (int)numericUpDownKernelSize.Value;
GK.sigma_y = (int)numericUpDownKernelSize.Value;
GK.sigma_z = (int)numericUpDownKernelSize.Value;
GK.Run();
cImage K = GK.GetOutPut();
if (Parent.comboBoxAxeY.SelectedIndex == -1) return;
if (Parent.comboBoxVolume.SelectedIndex == -1) return;
cExtendedList ListVolumes = new cExtendedList();
ListX.Clear();
ListY.Clear();
ListZ.Clear();
cExtendedTable TableForDataToBeAnalyzed = Parent.GetActiveSignatures(false);
for (int j = 0; j < TableForDataToBeAnalyzed[0].Count; j++)
{
ListX.Add(TableForDataToBeAnalyzed[Parent.comboBoxAxeX.SelectedIndex][j]);
ListY.Add(TableForDataToBeAnalyzed[Parent.comboBoxAxeY.SelectedIndex][j]);
}
//MaxX = ListX.Max();
//MinX = ListX.Min();
//MaxY = ListY.Max();
//MinY = ListY.Min();
MaxX = Parent.chartForPoints.ChartAreas[0].AxisX.Maximum;
MinX = Parent.chartForPoints.ChartAreas[0].AxisX.Minimum;
MaxY = Parent.chartForPoints.ChartAreas[0].AxisY.Maximum;
MinY = Parent.chartForPoints.ChartAreas[0].AxisY.Minimum;
//MaxY = Parent.MaxY;
//MinY = Parent.MinY;
if (this.radioButton3D.Checked)
{
for (int j = 0; j < TableForDataToBeAnalyzed[0].Count; j++)
{
ListZ.Add(TableForDataToBeAnalyzed[Parent.comboBoxVolume.SelectedIndex][j]);
}
MaxZ = ListZ.Max();
MinZ = ListZ.Min();
}
DensityMaps = new cImage(ImageWidth, ImageHeight, ImageDepth, cGlobalInfo.ListCellularPhenotypes.Count);
int[] ClassPopulations = new int[cGlobalInfo.ListCellularPhenotypes.Count];
if (this.radioButton3D.Checked)
{
int Idx = 0;
for (int j = 0; j < Parent.InputTable[0].Count; j++)
{
if (Parent.PanelPhenotypeSelection.GetListSelectedClass()[(int)Parent.MachineLearning.Classes[j]])
{
double TmpValueX = (ImageWidth * (ListX[Idx] - MinX)) / (MaxX - MinX) - K.Width / 2;
double TmpValueY = ImageHeight - (ImageHeight * (ListY[Idx] - MinY)) / (MaxY - MinY) - K.Height / 2;
double TmpValueZ = ImageDepth - (ImageDepth * (ListZ[Idx] - MinZ)) / (MaxZ - MinZ) - K.Depth / 2;
DensityMaps.AddInto(K, (int)TmpValueX, (int)TmpValueY, (int)TmpValueZ, (int)Parent.MachineLearning.Classes[j]);
ClassPopulations[(int)Parent.MachineLearning.Classes[j]]++;
Idx++;
}
}
}
else
{
int Idx = 0;
for (int j = 0; j < Parent.InputTable[0].Count; j++)
{
if (Parent.PanelPhenotypeSelection.GetListSelectedClass()[(int)Parent.MachineLearning.Classes[j]])
{
double TmpValueX = (ImageWidth * (ListX[Idx] - MinX)) / (MaxX - MinX) - K.Width / 2;
double TmpValueY = ImageHeight - (ImageHeight * (ListY[Idx] - MinY)) / (MaxY - MinY) - K.Height / 2;
DensityMaps.AddInto(K, (int)TmpValueX, (int)TmpValueY, 0, (int)Parent.MachineLearning.Classes[j]);
ClassPopulations[(int)Parent.MachineLearning.Classes[j]]++;
Idx++;
}
}
}
cListExtendedTable TablesForDensity = new cListExtendedTable(DensityMaps);
for (int idxChannel = 0; idxChannel < DensityMaps.GetNumChannels(); idxChannel++)
{
DensityMaps.SingleChannelImage[idxChannel].Name = cGlobalInfo.ListCellularPhenotypes[idxChannel].Name;
float Sum = 1;
if (checkBoxNormalized.Checked)
{
Sum = (float)TablesForDensity[idxChannel].Sum();
if (Sum <= 0.0) continue;
for (int i = 0; i < DensityMaps.SingleChannelImage[idxChannel].Data.Length; i++)
{
//if (ClassPopulations[idxChannel] > 0)
DensityMaps.SingleChannelImage[idxChannel].Data[i] = (100 * DensityMaps.SingleChannelImage[idxChannel].Data[i]) / Sum;
}
}
else
{
for (int i = 0; i < DensityMaps.SingleChannelImage[idxChannel].Data.Length; i++)
{
// if (ClassPopulations[idxChannel] > 0)
DensityMaps.SingleChannelImage[idxChannel].Data[i] = DensityMaps.SingleChannelImage[idxChannel].Data[i];
}
}
}
cDisplaySingleImage IV = new cDisplaySingleImage();
DensityMaps.Name = "Density Maps. K["+ this.numericUpDownKernelSize.Value +"]";
if (this.checkBoxModifyColors.Checked)
IV.ListLinearMaxColor = new List<Color>();
int RealIdxChannel = 0;
for (int idxChannel = 0; idxChannel < ClassPopulations.Length; idxChannel++)
{
if (ClassPopulations[idxChannel] == 0)
DensityMaps.SingleChannelImage.RemoveAt(RealIdxChannel--);
else
{
if (this.checkBoxModifyColors.Checked)
IV.ListLinearMaxColor.Add(cGlobalInfo.ListCellularPhenotypes[idxChannel].ColourForDisplay);
}
RealIdxChannel++;
}
IV.SetInputData(DensityMaps);
IV.Run();
this.buttonApply.Enabled = true;
}
