private void backgroundWorkerForCSVtoDB_DoWork(object sender, DoWorkEventArgs e)
{
BackgroundWorker worker = sender as BackgroundWorker;
CSVsr = new CsvFileReader(PathName);
CSVsr.Separator = this.Delimiter.ToCharArray()[0];
CsvRow OriginalNames = new CsvRow();
if (!CSVsr.ReadRow(OriginalNames))
{
CSVsr.Close();
return;
}
int ColPlateName = GetColIdxFor("Plate name", CSVWindow);
int ColCol = GetColIdxFor("Column", CSVWindow);
int ColRow = GetColIdxFor("Row", CSVWindow);
int ColWellPos = GetColIdxFor("Well position", CSVWindow);
int ColPhenotypeClass = GetColIdxFor("Phenotype Class", CSVWindow);
int[] ColsForDescriptors = GetColsIdxFor("Descriptor", CSVWindow);
FormForProgress ProgressWindow = new FormForProgress();
ProgressWindow.Text = "CSV -> DB : processing";
ProgressWindow.Show();
CsvRow CurrentDesc = new CsvRow();
int TotalPlateNumber = 0;
int TotalObjectNumber = 0;
int TotalWellNumber = 0;
string OriginalPlatePlateName;
string CurrentPlateName;
string ConvertedName;
this.CompleteReportString += "Source file: " + PathName + "\n";
this.CompleteReportString += OriginalNames.Count + " features selected.\n";
this.CompleteReportString += "Time stamp: " + DateTime.Now.ToString() + " \n";
if (CSVsr.ReadRow(CurrentDesc) == false) return;
do
{
if (ColPlateName == -1)
{
ConvertedName = OriginalPlatePlateName = CurrentPlateName = "Generated Plate Name";
}
else
{
OriginalPlatePlateName = CurrentDesc[ColPlateName];
CurrentPlateName = CurrentDesc[ColPlateName];
ConvertedName = "";
foreach (var c in System.IO.Path.GetInvalidFileNameChars())
ConvertedName = OriginalPlatePlateName.Replace(c, '-');
}
List<string> ListNameSignature = new List<string>();
for (int idxDesc = 0/*Mode + 1*/; idxDesc < ColsForDescriptors.Length/* + Mode + 1*/; idxDesc++)
{
string TmpSignature = OriginalNames[ColsForDescriptors[idxDesc]];
TmpSignature = TmpSignature.Replace('[', '_');
TmpSignature = TmpSignature.Replace(']', '_');
ListNameSignature.Add(TmpSignature);
}
ListNameSignature.Add("Phenotype_Class");
ListNameSignature.Add("Phenotype_Confidence");
cSQLiteDatabase SQDB = new cSQLiteDatabase(SelectedPath + "\\" + ConvertedName, ListNameSignature, true);
this.CompleteReportString += "\n" + CurrentPlateName + ":\n";
TotalPlateNumber++;
do
{
string OriginalWellPos;
int[] Pos = new int[2];
if (Mode == 1)
{
Pos = ConvertPosition(CurrentDesc[ColWellPos]);
if (Pos == null)
{
if (MessageBox.Show("Error in converting the current well position.\nGo to Edit->Options->Import-Export->Well Position Mode to fix this.\nDo you want continue ?", "Loading error !", MessageBoxButtons.YesNo, MessageBoxIcon.Error) == System.Windows.Forms.DialogResult.No)
{
CSVsr.Close();
return;
}
//else
// goto NEXTLOOP;
}
OriginalWellPos = CurrentDesc[ColWellPos];
}
else
{
if (int.TryParse(CurrentDesc[ColCol], out Pos[0]) == false)
goto NEXTLOOP;
if (int.TryParse(CurrentDesc[ColRow], out Pos[1]) == false)
goto NEXTLOOP;
OriginalWellPos = ConvertPosition(int.Parse(CurrentDesc[ColCol]), int.Parse(CurrentDesc[ColRow]));// "("+CurrentDesc[ColCol]+","+CurrentDesc[ColRow]+")";
}
string CurrentWellPos = OriginalWellPos;
cWellForDatabase WellForDB = new cWellForDatabase(OriginalPlatePlateName, Pos[0], Pos[1]);
cExtendedTable ListData = new cExtendedTable();
// for (int idxDesc = 0; idxDesc < ColsForDescriptors.Length; idxDesc++)
// ListData[idxDesc] = new List<double>();
ProgressWindow.richTextBoxForComment.AppendText(CurrentPlateName + " : " + CurrentWellPos + "\n");
//ProgressWindow.label.Refresh();
ProgressWindow.Refresh();
do
{
// CurrentWellPos = CurrentDesc[ColWellPos];
cExtendedList Signature = new cExtendedList();
for (int idxDesc = 0; idxDesc < ColsForDescriptors.Length; idxDesc++)
{
double Value;
if (double.TryParse(CurrentDesc[ColsForDescriptors[idxDesc]], NumberStyles.Any, CultureInfo.InvariantCulture/*.CreateSpecificCulture("en-US")*/, out Value))
{
if (double.IsNaN(Value))
Signature.Add(0);
else
Signature.Add(Value);
}
else
{
Signature.Add(0);
}
}
// if the class of the phenotype is defined in the file then use it
// if not, put it at 0
double ValueClass;
if ((ColPhenotypeClass != -1) && (double.TryParse(CurrentDesc[ColPhenotypeClass], out ValueClass) == true))
{
double IntValue = (int)(ValueClass) % cGlobalInfo.ListCellularPhenotypes.Count;
Signature.Add(IntValue);
}
else
{
Signature.Add(0);
}
// finally add the classification confidence column (1 by default)
Signature.Add(1);
ListData.Add(Signature);
// WellForDB.AddSignature(Signature);
// manage the end of the file
if (CSVsr.ReadRow(CurrentDesc) == false)
{
WellForDB.AddListSignatures(ListData);
cFeedBackMessage FeedBackMessage = SQDB.AddNewWell(WellForDB);
SQDB.CloseConnection();
// this.CompleteReportString += FeedBackMessage.Message + "\n";
goto NEXTLOOP;
}
if (ColPlateName == -1)
CurrentPlateName = "Generated Plate Name";
else
CurrentPlateName = CurrentDesc[ColPlateName];
if (Mode == 1)
CurrentWellPos = CurrentDesc[ColWellPos];
else
{
int ResCol;
int ResRow;
if ((!int.TryParse(CurrentDesc[ColCol], out ResCol)) || (!int.TryParse(CurrentDesc[ColRow], out ResRow))) goto NEXTLOOP;
CurrentWellPos = ConvertPosition(ResCol, ResRow);
}
TotalObjectNumber++;
// NEXTSIGNATURE: ;
} while (CurrentWellPos == OriginalWellPos);
TotalWellNumber++;
WellForDB.AddListSignatures(ListData);
SQDB.AddNewWell(WellForDB);
ReportTable.ListRowNames.Add(CurrentPlateName + " : " + CurrentWellPos);
ReportTable[0].Add(ListData.Count);
ReportTable[0].ListTags.Add(CurrentPlateName + " : " + CurrentWellPos + "\n" + ListData.Count + " objects");
this.CompleteReportString += "\t" + CurrentWellPos + " : " + ListData.Count + " objects\n";
NEXTSIGNATURE: ;
} while (OriginalPlatePlateName == CurrentPlateName);
SQDB.CloseConnection();
} while (true);
NEXTLOOP: ;
ProgressWindow.Close();
this.CompleteReportString += "\n-----------------------------\n";
this.CompleteReportString += TotalPlateNumber + " plates\n";
this.CompleteReportString += TotalWellNumber + " wells\n";
this.CompleteReportString += TotalObjectNumber + " objects\n";
this.CompleteReportString += "\nDataBase location:\n" + SelectedPath;
// worker.ReportProgress(10);
}
private void HarmonyToDB(string DefaultPath)
{
#region Get the directory
if (!Directory.Exists(DefaultPath)) DefaultPath = "";
var dlg1 = new Ionic.Utils.FolderBrowserDialogEx();
dlg1.Description = "Select the folder of your experiment.";
dlg1.ShowNewFolderButton = true;
dlg1.ShowEditBox = true;
if (DefaultPath != "")
dlg1.SelectedPath = DefaultPath;
//dlg1.NewStyle = false;
//dlg1.SelectedPath = txtExtractDirectory.Text;
dlg1.ShowFullPathInEditBox = true;
dlg1.RootFolder = System.Environment.SpecialFolder.Desktop;
// Show the FolderBrowserDialog.
DialogResult result = dlg1.ShowDialog();
if (result != DialogResult.OK) return;
string Path = dlg1.SelectedPath;
if (Directory.Exists(Path) == false) return;
#endregion
#region Get the different files
string[] ListFilesForPlates = null;
try
{
ListFilesForPlates = Directory.GetFiles(Path, "Objects_Population - *.txt", SearchOption.AllDirectories);
}
catch (System.Exception excep)
{
MessageBox.Show(excep.Message, "Error!", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
if (ListFilesForPlates.Length == 0)
{
MessageBox.Show("The selected directory do not contain any Objects_Population files !", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
string[] Sep = new string[1];
Sep[0] = "\\";
Dictionary<string, string> CurrentPlateDico = new Dictionary<string, string>();
// string[] FirstListImages = Directory.GetFiles(PlateDirectories[i], TmpPlateName + "_*.C01", SearchOption.AllDirectories);
foreach (var item in ListFilesForPlates)
{
string[] Res = item.Split(Sep, StringSplitOptions.RemoveEmptyEntries);
string CurrentName = Res[Res.Length-1];
if (CurrentPlateDico.ContainsKey(CurrentName.Remove(CurrentName.Length - 4))) continue;
CurrentPlateDico.Add(CurrentName.Remove(CurrentName.Length-4), item);
}
string[] ListTypes = CurrentPlateDico.Keys.ToArray();
// plates selection GUI
FormForPlateSelection FFP = new FormForPlateSelection(ListTypes,false);
FFP.Text = "Object Types Selection";
if (FFP.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
ListFilesForPlates = FFP.GetListPlatesSelected();
#endregion
if (ListFilesForPlates.Length == 0) return;
ListFilesForPlates = Directory.GetFiles(Path, ListFilesForPlates[0] + ".txt", SearchOption.AllDirectories);
#region And now let's analyse the files adn create the CSV
CsvRow CurrentRow = new CsvRow();
bool IsHeaderWritten = false;
string OriginalHeader = "";
Sep[0] = "\\";
string[] TmpSplit = ListFilesForPlates[0].Split(Sep, StringSplitOptions.RemoveEmptyEntries);
//TmpSplit[TmpSplit.Length-1].Replace(".txt",".csv");
string TPath = Path + "\\" + TmpSplit[TmpSplit.Length - 1].Replace(".txt", ".csv");
Sep[0] = ","; // specifically for the bounding box processing
FormForProgress MyProgressBar = new FormForProgress();
MyProgressBar.progressBar.Maximum = ListFilesForPlates.Length;
MyProgressBar.Show();
for (int i = 0; i < ListFilesForPlates.Length ; i++)
{
MyProgressBar.richTextBoxForComment.AppendText(ListFilesForPlates[i]);
MyProgressBar.richTextBoxForComment.Update();
StreamWriter stream = new StreamWriter(TPath, true, Encoding.ASCII);
#region process the header
string CurrentFile = ListFilesForPlates[i];
CsvFileReader CSVReader = new CsvFileReader(CurrentFile);
CSVReader.Separator = '\t';
CSVReader.ReadRow(CurrentRow);
// let's take care of the header first
while (CurrentRow[0]!="Plate Name")
{
CSVReader.ReadRow(CurrentRow);
}
string PlateName = CurrentRow[1];
// skip the rest of the header
while (CurrentRow[0] != "[Data]")
{
CSVReader.ReadRow(CurrentRow);
}
// read the columns names
CSVReader.ReadRow(CurrentRow);
List<string> Descs = CurrentRow;
string TobeWritten = "Plate Name,";
int IdxBoundingBox = -1;
int IndexCol = -1;
int IndexRow = -1;
int IndexCompound = -1;
int IndexConcentration = -1;
int IndexCellcount = -1;
int NumDesc = Descs.Count;
for (int j = 0; j < Descs.Count; j++)
{
if (Descs[j] == "Bounding Box")
{
TobeWritten += "X_Min,Y_Min,X_Max,Y_Max,";
IdxBoundingBox = j;
// NumDesc += 3;
}
else if (Descs[j] == "Row")
{
IndexRow = j;
TobeWritten += "Well Position,";
}
else if (Descs[j] == "Column")
{
IndexCol = j;
}
else if (Descs[j] == "Compound")
{
// skipped
IndexCompound = j;
}
else if (Descs[j] == "Concentration")
{
// skipped
IndexConcentration = j;
}
else if (Descs[j] == "Cell Count")
{
// skipped
IndexCellcount = j;
}
else
TobeWritten += Descs[j] + ",";
}
TobeWritten = TobeWritten.Remove(TobeWritten.Length - 1);
if (IsHeaderWritten == false)
{
OriginalHeader = TobeWritten;
stream.WriteLine(TobeWritten);
IsHeaderWritten = true;
}
else
{
// inconsistency between the headers... skip the plate
if (TobeWritten != OriginalHeader)
{
continue;
}
}
#endregion
// now let's process the data
int IdxRow = 0;
while (!CSVReader.EndOfStream)
{
CSVReader.ReadRow(CurrentRow);
TobeWritten = PlateName+",";
for (int j = 0; j < Descs.Count; j++)
{
if ((IdxBoundingBox > -1) && (j == IdxBoundingBox))
{
// let's process the bounding box
string BB = CurrentRow[j];
BB = BB.Remove(BB.Length - 1);
BB = BB.Remove(0, 1);
string[] Splitted = BB.Split(Sep, StringSplitOptions.None);
TobeWritten += Splitted[0] + "," + Splitted[1] + "," + Splitted[2] + "," + Splitted[3] + ",";
// j += 3;
}
else if (j == IndexRow)
{
TobeWritten += ConvertPosition(int.Parse(CurrentRow[IndexCol]), int.Parse(CurrentRow[IndexRow]))+",";
}
else if ((j == IndexCol)||(j==IndexCellcount)||(j==IndexCompound)||(j==IndexConcentration))
{
// do nothing
}
else
{
if (CurrentRow[j] != "")
TobeWritten += CurrentRow[j] + ",";
else
TobeWritten += "NaN,";
}
}
TobeWritten = TobeWritten.Remove(TobeWritten.Length - 1);
stream.WriteLine(TobeWritten );
IdxRow++;
}
CSVReader.Close();
stream.Dispose();
MyProgressBar.progressBar.Value++;
MyProgressBar.progressBar.Update();
}
MyProgressBar.Close();
#endregion
#region let's build the database now
// if (CSVFeedBackWindow == null) return;
// if (CSVFeedBackWindow.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
string DBPath = Path + "\\DB";
Directory.CreateDirectory(DBPath);
cConvertCSVtoDB CCTODB = CSVtoDB(TPath, ",", DBPath);
if (CCTODB == null)
{
return;
}
else
{
// update image accessor
cGlobalInfo.OptionsWindow.radioButtonImageAccessDefined.Checked = false;
cGlobalInfo.OptionsWindow.radioButtonImageAccessHarmony35.Checked = true;
cGlobalInfo.OptionsWindow.textBoxImageAccesImagePath.Text = Path;
cGlobalInfoToBeExported GlobalInfoToBeExported = new cGlobalInfoToBeExported();
cGlobalInfo.OptionsWindow.TmpOptionPath = GlobalInfoToBeExported.Save(DBPath+"\\Options.opt");
//cGlobalInfo.OptionsWindow.sav
}
#endregion
}
private void TSItemSubPopSelectionDataTableImages(object sender, EventArgs e)
{
ToolStripMenuItem ParentTag = (ToolStripMenuItem)(sender);
List<int> MyList = ((List<int>)(ParentTag.Tag));
cExtendedTable ET = new cExtendedTable(this.InputSimpleData.Count, MyList.Count, 0);
for (int i = 0; i < this.InputSimpleData.Count; i++)
{
ET[i].Name = this.InputSimpleData[i].Name;
}
ET.ListRowNames = new List<string>();
for (int i = 0; i < MyList.Count; i++)
{
ET.ListRowNames.Add(i.ToString());
}
if (this.InputSimpleData.ListTags != null) ET.ListTags = new List<object>();
int IdxPt = 0;
FormForProgress FP = new FormForProgress();
FP.Show();
int MaxProgress = MyList.Count;
FP.progressBar.Maximum = MaxProgress;
foreach (var item in MyList)
{
for (int i = 0; i < this.InputSimpleData.Count; i++)
{
ET[i][IdxPt] = this.InputSimpleData[i][MyList[IdxPt]];
}
if ((this.InputSimpleData.ListTags != null) && (this.InputSimpleData.ListTags[IdxPt] != null))
{
if (this.InputSimpleData.ListTags[MyList[IdxPt]].GetType() == typeof(cSingleBiologicalObject))
{
cSingleBiologicalObject TmpBioObj = ((cSingleBiologicalObject)this.InputSimpleData.ListTags[MyList[IdxPt]]);
List<cImageMetaInfo> ListMeta = cGlobalInfo.ImageAccessor.GetImageInfo(TmpBioObj);
if (ListMeta==null) continue;
cImage Image = new cImage(ListMeta);
TmpBioObj.BD_BoxMax.Z = TmpBioObj.BD_BoxMin.Z = 0;
cImage CroppedImaged = Image.Crop(TmpBioObj.BD_BoxMin, TmpBioObj.BD_BoxMax);
if((cGlobalInfo.TmpImageDisplayProperties==null)||(cGlobalInfo.TmpImageDisplayProperties.ListMin.Count != CroppedImaged.GetNumChannels()))
{
ET.ListTags.Add(CroppedImaged.GetBitmap(1f, null, null));
}
else
{
cImageDisplayProperties IP = cGlobalInfo.TmpImageDisplayProperties;
ET.ListTags.Add(CroppedImaged.GetBitmap(1f, IP, null));
}
FP.richTextBoxForComment.AppendText("Object "+ IdxPt +" / "+MyList.Count +"\n");
}
}
FP.progressBar.Value = IdxPt;
FP.Refresh();
IdxPt++;
}
FP.Close();
ET.Name = "Data Table - " + MyList.Count + " Objects";
cDisplayExtendedTable DET = new cDisplayExtendedTable();
DET.SetInputData(ET);
DET.Run();
//DataPoint DP = new DataPoint();
//if (this.InputSimpleData[0].ListTags != null)
//{
// if (j >= this.InputSimpleData[0].ListTags.Count) continue;
// DP.Tag = this.InputSimpleData[0].ListTags[j];
// // if (DP.Tag.GetType() == typeof(cWell))
// // {
// // DP.Color = ((cWell)(DP.Tag)).GetClassColor();
// // DP.ToolTip = ((cWell)(DP.Tag)).GetShortInfo() + Value[0];
// // }
// if (DP.Tag.GetType() == typeof(cSingleBiologicalObject))
// {
// // DP.Color = ((cSingleBiologicalObject)(DP.Tag)).GetColor();
// // DP.ToolTip = ((cSingleBiologicalObject)(DP.Tag)).GetAssociatedPhenotype().Name + "\nValue: (" + DP.XValue.ToString("N2") + ":" + DP.YValues[0].ToString("N2") + ")";
// }
//}
}
private void generateDBFromCSVToolStripMenuItem_Click(object sender, EventArgs e)
{
OpenFileDialog CurrOpenFileDialog = new OpenFileDialog();
CurrOpenFileDialog.Filter = "csv files (*.csv)|*.csv";//|db files (*.db)|*.db|nc files (*.nc)|*.nc
CurrOpenFileDialog.Multiselect = false;
DialogResult Res = CurrOpenFileDialog.ShowDialog();
if (Res != DialogResult.OK) return;
FormForImportExcel CSVWindow = CellByCellFromCSV(CurrOpenFileDialog.FileNames[0]);
if (CSVWindow == null) return;
if (CSVWindow.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
if (CompleteScreening != null) CompleteScreening.Close3DView();
FolderBrowserDialog WorkingFolderDialog = new FolderBrowserDialog();
WorkingFolderDialog.ShowNewFolderButton = true;
WorkingFolderDialog.Description = "Select the working directory";
if (WorkingFolderDialog.ShowDialog() != DialogResult.OK) return;
//if (IsFileUsed(CurrOpenFileDialog.FileNames[0]))
//{
// MessageBox.Show("File currently used by another application.\n", "Loading error !", MessageBoxButtons.OK, MessageBoxIcon.Error);
// return;
//}
//Microsoft.Research.Science.Data.DataSet Datacsv = Microsoft.Research.Science.Data.CSV.CsvDataSet.Open(CurrOpenFileDialog.FileNames[0]);
//int NumDesc = Datacsv.Variables.Count;
//for (int IdxDesc = 0; IdxDesc < NumDesc; IdxDesc++)
//{
// var DescInfo = Datacsv.Variables[IdxDesc];
// string NameDesc = DescInfo.Name;
// var TypeData = DescInfo.TypeOfData;
// string DataName = TypeData.Name;
//}
int NumPlateName = 0;
int NumRow = 0;
int NumCol = 0;
int NumWellPos = 0;
// int NumLocusID = 0;
// int NumConcentration = 0;
// int NumName = 0;
// int NumInfo = 0;
// int NumClass = 0;
int numDescritpor = 0;
for (int i = 0; i < CSVWindow.dataGridViewForImport.Rows.Count; i++)
{
string CurrentVal = CSVWindow.dataGridViewForImport.Rows[i].Cells[2].Value.ToString();
if ((CurrentVal == "Plate name") && ((bool)CSVWindow.dataGridViewForImport.Rows[i].Cells[1].Value))
NumPlateName++;
if ((CurrentVal == "Row") && ((bool)CSVWindow.dataGridViewForImport.Rows[i].Cells[1].Value))
NumRow++;
if ((CurrentVal == "Column") && ((bool)CSVWindow.dataGridViewForImport.Rows[i].Cells[1].Value))
NumCol++;
if ((CurrentVal == "Well position") && ((bool)CSVWindow.dataGridViewForImport.Rows[i].Cells[1].Value))
NumWellPos++;
if ((CurrentVal == "Descriptor") && ((bool)CSVWindow.dataGridViewForImport.Rows[i].Cells[1].Value))
numDescritpor++;
}
if (NumPlateName != 1)
{
MessageBox.Show("One and only one \"Plate Name\" has to be selected", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
if ((NumRow != 1) && (GlobalInfo.OptionsWindow.radioButtonWellPosModeDouble.Checked == true))
{
MessageBox.Show("One and only one \"Row\" has to be selected", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
if ((NumCol != 1) && (GlobalInfo.OptionsWindow.radioButtonWellPosModeDouble.Checked == true))
{
MessageBox.Show("One and only one \"Column\" has to be selected", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
if ((NumWellPos != 1) && (GlobalInfo.OptionsWindow.radioButtonWellPosModeSingle.Checked == true))
{
MessageBox.Show("One and only one \"Well position\" has to be selected", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
if ((numDescritpor < 1) && (CSVWindow.IsImportCSV))
{
MessageBox.Show("You need to select at least one \"Descriptor\" !", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
int Mode = 2;
if (GlobalInfo.OptionsWindow.radioButtonWellPosModeSingle.Checked) Mode = 1;
CsvFileReader CSVsr = new CsvFileReader(CurrOpenFileDialog.FileNames[0]);
CsvRow OriginalNames = new CsvRow();
if (!CSVsr.ReadRow(OriginalNames))
{
CSVsr.Close();
return;
}
int ColPlateName = GetColIdxFor("Plate name", CSVWindow);
int ColCol = GetColIdxFor("Column", CSVWindow);
int ColRow = GetColIdxFor("Row", CSVWindow);
int ColWellPos = GetColIdxFor("Well position", CSVWindow);
int[] ColsForDescriptors = GetColsIdxFor("Descriptor", CSVWindow);
int WellLoaded = 0;
int FailToLoad = 0;
// CompleteScreening.Columns = (int)CSVWindow.numericUpDownColumns.Value;
// CompleteScreening.Rows = (int)CSVWindow.numericUpDownRows.Value;
// CompleteScreening.ListDescriptors.Clean();
FormForProgress ProgressWindow = new FormForProgress();
ProgressWindow.Show();
CsvRow CurrentDesc = new CsvRow();
if (CSVsr.ReadRow(CurrentDesc) == false) return;
do
{
string OriginalPlatePlateName = CurrentDesc[ColPlateName];
string CurrentPlateName = CurrentDesc[ColPlateName];
string ConvertedName = "";
foreach (var c in System.IO.Path.GetInvalidFileNameChars())
{
ConvertedName = OriginalPlatePlateName.Replace(c, '-');
}
List<string> ListNameSignature = new List<string>();
for (int idxDesc = Mode + 1; idxDesc < ColsForDescriptors.Length + Mode + 1; idxDesc++)
ListNameSignature.Add(OriginalNames[idxDesc]);
cSQLiteDatabase SQDB = new cSQLiteDatabase(WorkingFolderDialog.SelectedPath + "\\" + ConvertedName, ListNameSignature, true);
do
{
string OriginalWellPos = CurrentDesc[ColWellPos];
string CurrentWellPos = OriginalWellPos;
int[] Pos = new int[2];
if (Mode == 1)
{
Pos = ConvertPosition(CurrentDesc[ColWellPos]);
if (Pos == null)
{
if (MessageBox.Show("Error in converting the current well position.\nGo to Edit->Options->Import-Export->Well Position Mode to fix this.\nDo you want continue ?", "Loading error !", MessageBoxButtons.YesNo, MessageBoxIcon.Error) == System.Windows.Forms.DialogResult.No)
{
CSVsr.Close();
return;
}
//else
// goto NEXTLOOP;
}
}
else
{
//if (int.TryParse(CurrentDesc[ColCol], out Pos[0]) == false)
// // goto NEXTLOOP;
//if (int.TryParse(CurrentDesc[ColRow], out Pos[1]) == false)
// goto NEXTLOOP;
}
cWellForDatabase WellForDB = new cWellForDatabase(OriginalPlatePlateName, Pos[0], Pos[1]);
List<List<double>> ListData = new List<List<double>>();
// for (int idxDesc = 0; idxDesc < ColsForDescriptors.Length; idxDesc++)
// ListData[idxDesc] = new List<double>();
ProgressWindow.label.Text = OriginalWellPos;
ProgressWindow.label.Refresh();
do
{
// CurrentWellPos = CurrentDesc[ColWellPos];
List<double> Signature = new List<double>();
for (int idxDesc = 0; idxDesc < ColsForDescriptors.Length; idxDesc++)
{
double Value;
if ((double.TryParse(CurrentDesc[ColsForDescriptors[idxDesc]], out Value)) && (!double.IsNaN(Value)))
{
//cDescriptor CurrentDescriptor = new cDescriptor(Value, CompleteScreening.ListDescriptors[idxDesc/* + ShiftIdx*/], CompleteScreening);
Signature.Add(Value);
}
/*else
{
FailToLoad++;
goto NEXTLOOP;
}*/
}
ListData.Add(Signature);
// WellForDB.AddSignature(Signature);
if (CSVsr.ReadRow(CurrentDesc) == false)
{
WellForDB.AddListSignatures(ListData);
SQDB.AddNewWell(WellForDB);
SQDB.CloseConnection();
goto NEXTLOOP;
}
CurrentPlateName = CurrentDesc[ColPlateName];
CurrentWellPos = CurrentDesc[ColWellPos];
} while (CurrentWellPos == OriginalWellPos);
WellForDB.AddListSignatures(ListData);
SQDB.AddNewWell(WellForDB);
} while (OriginalPlatePlateName == CurrentPlateName);
SQDB.CloseConnection();
} while (true);
NEXTLOOP: ;
ProgressWindow.Close();
FormForPlateDimensions PlateDim = new FormForPlateDimensions();
PlateDim.Text = "Load generated screening";
PlateDim.checkBoxAddCellNumber.Visible = true;
PlateDim.checkBoxIsOmitFirstColumn.Visible = true;
PlateDim.labelHisto.Visible = true;
PlateDim.numericUpDownHistoSize.Visible = true;
if (PlateDim.ShowDialog() != System.Windows.Forms.DialogResult.OK)
return;
LoadCellByCellDB(PlateDim, WorkingFolderDialog.SelectedPath);
}
private void AverageOperationsToDescriptorItem(object sender, EventArgs e)
{
FormForDescOperations MainWindow = new FormForDescOperations(cGlobalInfo.CurrentScreening.ListDescriptors.GetListNames());
MainWindow.Text = "Average Based Operations";
if (MainWindow.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
string NewDescName = MainWindow.textBoxNewDescName.Text;
cDescriptorType DescType1 = cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorByName(MainWindow.comboBoxDescriptor1.Text);
cDescriptorType DescType2 = cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorByName(MainWindow.comboBoxDescriptor2.Text);
if ((DescType1 == null) || (DescType2 == null)) return;
FormForProgress ProgressWindow = new FormForProgress();
ProgressWindow.Show();
int IdxProgress = 1;
int MaxProgress = cGlobalInfo.CurrentScreening.ListPlatesAvailable.Count;
ProgressWindow.progressBar.Maximum = MaxProgress;
cDescriptorType NewDescType = new cDescriptorType(NewDescName, true, 1);
cGlobalInfo.CurrentScreening.ListDescriptors.AddNew(NewDescType);
eBinaryOperationType PostProcessBinaryOp = eBinaryOperationType.UNDEFINED;
if (MainWindow.checkBoxActivePostProcess.Checked)
{
switch (MainWindow.domainUpDownPostProcessOperator.Text)
{
case "*":
PostProcessBinaryOp = eBinaryOperationType.MULTIPLY;
break;
case "+":
PostProcessBinaryOp = eBinaryOperationType.ADD;
break;
case "/":
PostProcessBinaryOp = eBinaryOperationType.DIVIDE;
break;
case "-":
PostProcessBinaryOp = eBinaryOperationType.SUBSTRACT;
break;
default:
return;
}
}
if (MainWindow.tabControlMain.SelectedTab.Name == "tabPageBinary")
{
// SingleCellOperation.ListDualOperations = new List<eBinaryOperationType>();
// eDualOperationType OperationType = eDualOperationType.ADD;
eBinaryOperationType BinaryOp = eBinaryOperationType.ADD;
switch (MainWindow.domainUpDown1.Text)
{
case "*":
BinaryOp = eBinaryOperationType.MULTIPLY;
break;
case "+":
BinaryOp = eBinaryOperationType.ADD;
break;
case "/":
BinaryOp = eBinaryOperationType.DIVIDE;
break;
case "-":
BinaryOp = eBinaryOperationType.SUBSTRACT;
break;
default:
return;
}
foreach (cPlate CurrentPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
foreach (cWell Tmpwell in CurrentPlate.ListActiveWells)
{
cListSignature LDesc = new cListSignature();
cSignature NewDesc = null;
double Val = 0;
switch (BinaryOp)
{
case eBinaryOperationType.ADD:
Val = Tmpwell.GetAverageValue(DescType1) + Tmpwell.GetAverageValue(DescType2);
break;
case eBinaryOperationType.MULTIPLY:
Val = Tmpwell.GetAverageValue(DescType1) * Tmpwell.GetAverageValue(DescType2);
break;
case eBinaryOperationType.SUBSTRACT:
Val = Tmpwell.GetAverageValue(DescType1) - Tmpwell.GetAverageValue(DescType2);
break;
case eBinaryOperationType.DIVIDE:
double denominator = Tmpwell.GetAverageValue(DescType2);
if (denominator == 0) Val = 0;
else Val = Tmpwell.GetAverageValue(DescType1) / denominator;
break;
default:
break;
}
if (PostProcessBinaryOp != eBinaryOperationType.UNDEFINED)
{
double ValuePostProcess = (double)MainWindow.numericUpDownPostProcessValue.Value;
switch (PostProcessBinaryOp)
{
case eBinaryOperationType.ADD:
Val += ValuePostProcess;
break;
case eBinaryOperationType.SUBSTRACT:
Val -= ValuePostProcess;
break;
case eBinaryOperationType.MULTIPLY:
Val *= ValuePostProcess;
break;
case eBinaryOperationType.DIVIDE:
if (ValuePostProcess == 0)
Val = 0;
else
Val /= ValuePostProcess;
break;
default:
break;
}
}
NewDesc = new cSignature(Val, NewDescType, cGlobalInfo.CurrentScreening);
LDesc.Add(NewDesc);
Tmpwell.AddSignatures(LDesc);
}
ProgressWindow.progressBar.Value = IdxProgress++;
ProgressWindow.richTextBoxForComment.AppendText(CurrentPlate.GetShortInfo());
ProgressWindow.Refresh();
}
}
#region unary operator
else
{
eUnaryOperationType OperationType = eUnaryOperationType.LOG;
if (MainWindow.radioButtonSQRT.Checked)
OperationType = eUnaryOperationType.SQRT;
else if (MainWindow.radioButtonLog.Checked)
OperationType = eUnaryOperationType.LOG;
else if (MainWindow.radioButtonABS.Checked)
OperationType = eUnaryOperationType.ABS;
else if (MainWindow.radioButtonEXP.Checked)
OperationType = eUnaryOperationType.EXP;
foreach (cPlate CurrentPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
foreach (cWell Tmpwell in CurrentPlate.ListActiveWells)
{
cListSignature LDesc = new cListSignature();
cSignature NewDesc = null;
double Val = 0;
switch (OperationType)
{
case eUnaryOperationType.LOG:
Val = Math.Log(Tmpwell.GetAverageValue(DescType1));
if (double.IsInfinity(Val) || double.IsNaN(Val)) Val = double.Epsilon;
break;
case eUnaryOperationType.SQRT:
Val = Tmpwell.GetAverageValue(DescType1);
if (Val < 0) Val = 0;
Val = Math.Sqrt(Val);
break;
case eUnaryOperationType.ABS:
Val = Math.Abs(Tmpwell.GetAverageValue(DescType1));
break;
case eUnaryOperationType.EXP:
Val = Math.Exp(Tmpwell.GetAverageValue(DescType1));
break;
default:
break;
}
if (PostProcessBinaryOp != eBinaryOperationType.UNDEFINED)
{
double ValuePostProcess = (double)MainWindow.numericUpDownPostProcessValue.Value;
switch (PostProcessBinaryOp)
{
case eBinaryOperationType.ADD:
Val += ValuePostProcess;
break;
case eBinaryOperationType.SUBSTRACT:
Val -= ValuePostProcess;
break;
case eBinaryOperationType.MULTIPLY:
Val *= ValuePostProcess;
break;
case eBinaryOperationType.DIVIDE:
if (ValuePostProcess == 0)
Val = 0;
else
Val /= ValuePostProcess;
break;
default:
break;
}
}
NewDesc = new cSignature(Val, NewDescType, cGlobalInfo.CurrentScreening);
LDesc.Add(NewDesc);
Tmpwell.AddSignatures(LDesc);
}
ProgressWindow.progressBar.Value = IdxProgress++;
ProgressWindow.richTextBoxForComment.AppendText(CurrentPlate.GetShortInfo());
ProgressWindow.Refresh();
}
}
#endregion
ProgressWindow.Close();
int IdxNull = 0;
foreach (cPlate TmpPlate in cGlobalInfo.CurrentScreening.ListPlatesActive)
{
foreach (cWell TmpWell in TmpPlate.ListActiveWells)
if (TmpWell.ListSignatures.Count != cGlobalInfo.CurrentScreening.ListDescriptors.Count)
IdxNull++;
}
if (IdxNull > 0)
System.Windows.Forms.MessageBox.Show("List signature count is different from list descriptor count", "Critical Error !", MessageBoxButtons.OK, MessageBoxIcon.Error);
cGlobalInfo.CurrentScreening.ListDescriptors.UpDateDisplay();
// CompleteScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < cGlobalInfo.CurrentScreening.ListPlatesAvailable.Count; idxP++)
cGlobalInfo.CurrentScreening.ListPlatesActive[idxP].UpDataMinMax();
StartingUpDateUI();
this.toolStripcomboBoxPlateList.Items.Clear();
for (int IdxPlate = 0; IdxPlate < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; IdxPlate++)
{
string Name = cGlobalInfo.CurrentScreening.ListPlatesActive.GetPlate(IdxPlate).GetName();
this.toolStripcomboBoxPlateList.Items.Add(Name);
PlateListWindow.listBoxPlateNameToProcess.Items.Add(Name);
PlateListWindow.listBoxAvaliableListPlates.Items.Add(Name);
}
cGlobalInfo.CurrentScreening.CurrentDisplayPlateIdx = 0;
cGlobalInfo.CurrentScreening.SetSelectionType(comboBoxClass.SelectedIndex - 1);
UpdateUIAfterLoading();
cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().DisplayDistribution(cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptor(), false);
}
public cFeedBackMessage Run()
{
if (this.Input == null)
{
FeedBackMessage.IsSucceed = false;
FeedBackMessage.Message = "No input data defined.";
return FeedBackMessage;
}
if (FilePath == "")
{
// user interface for file selection
SaveFileDialog CurrSaveFileDialog = new SaveFileDialog();
CurrSaveFileDialog.Filter = "CSV file (*.csv)|*.csv";
System.Windows.Forms.DialogResult Res = CurrSaveFileDialog.ShowDialog();
if (Res != System.Windows.Forms.DialogResult.OK)
return new cFeedBackMessage(false,this);
FilePath = CurrSaveFileDialog.FileName;
}
try
{
using (FileStream fs = new FileStream(FilePath, FileMode.OpenOrCreate))
{
}
}
catch (IOException ex)
{
MessageBox.Show("File currently used by another application.\n", "Saving error !", MessageBoxButtons.OK, MessageBoxIcon.Error);
return new cFeedBackMessage(false,this);
}
// create the file
string separator = ",";
List<cDescriptorType> ListSelectedDesc = cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveSingleCellDescriptors();
if (ListSelectedDesc.Count == 0)
{
MessageBox.Show("No single cell based descriptor selected.\n", "Saving error !", MessageBoxButtons.OK, MessageBoxIcon.Error);
return new cFeedBackMessage(false, this);
}
FormForProgress MyProgressBar = new FormForProgress();
MyProgressBar.progressBar.Maximum = this.Input.Count;
MyProgressBar.Show();
using (StreamWriter myFile = new StreamWriter(FilePath, false, Encoding.Default))
{
string HeaderToBeWritten = "Plate,Well,";
for (int i = 0; i < ListSelectedDesc.Count; i++)
{
HeaderToBeWritten += ListSelectedDesc[i].GetName() + separator;
}
HeaderToBeWritten += "Phenotype_Class";
myFile.WriteLine(HeaderToBeWritten);
int IdxWell = 0;
foreach(cWell TmpWell in this.Input)
{
cListWells TmpList = new cListWells(TmpWell);
// this table should contain all the selected descriptor values and the phenotypic classes
cExtendedTable CompleteTable = TmpList.GetSingleObjectDescriptorValuesFull(ListSelectedDesc);
HeaderToBeWritten = TmpWell.AssociatedPlate.GetName() + separator;
HeaderToBeWritten += TmpWell.GetPos() + separator;
for (int Row = 0; Row < CompleteTable[0].Count; Row++)
{
string ToBeWritten = HeaderToBeWritten;
for (int i = 0; i < CompleteTable.Count - 1; i++)
ToBeWritten += CompleteTable[i][Row] + separator;
ToBeWritten += CompleteTable[CompleteTable.Count - 1][Row];
myFile.WriteLine(ToBeWritten);
}
MyProgressBar.progressBar.Value = IdxWell++;
MyProgressBar.richTextBoxForComment.Text = TmpWell.GetShortInfo();
MyProgressBar.Update();
}
myFile.Close();
}
MyProgressBar.Close();
return FeedBackMessage;
}
private void SingleCellOperationsToDescriptorItem(object sender, EventArgs e)
{
List<string> ListNamesDesc = new List<string>();
foreach (var item in cGlobalInfo.CurrentScreening.ListDescriptors)
{
if (item.GetDataType() != "Single")
{
ListNamesDesc.Add(item.GetName());
}
}
FormForDescOperations MainWindow = new FormForDescOperations(ListNamesDesc);
if (MainWindow.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
string NewDescName = MainWindow.textBoxNewDescName.Text;
cDescriptorType DescType1 = cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorByName(MainWindow.comboBoxDescriptor1.Text);
cDescriptorType DescType2 = cGlobalInfo.CurrentScreening.ListDescriptors.GetDescriptorByName(MainWindow.comboBoxDescriptor2.Text);
if ((DescType1 == null) || (DescType2 == null)) return;
FormForProgress ProgressWindow = new FormForProgress();
ProgressWindow.Show();
int IdxProgress = 1;
int MaxProgress = cGlobalInfo.CurrentScreening.ListPlatesAvailable.Count;
ProgressWindow.progressBar.Maximum = MaxProgress;
cDescriptorType NewDescType = new cDescriptorType(NewDescName, true, 256, true);
cGlobalInfo.CurrentScreening.ListDescriptors.AddNew(NewDescType);
//HCSAnalyzer.Classes.General_Types.cDBConnection.cSingleCellOperations SCO = new HCSAnalyzer.Classes.General_Types.cDBConnection.cSingleCellOperations()
cSingleCellOperations SingleCellOperation = new cSingleCellOperations();
if (MainWindow.tabControlMain.SelectedTab.Name == "tabPageBinary")
{
SingleCellOperation.ListDualOperations = new List<eBinaryOperationType>();
// eDualOperationType OperationType = eDualOperationType.ADD;
switch (MainWindow.domainUpDown1.Text)
{
case "*":
SingleCellOperation.ListDualOperations.Add(eBinaryOperationType.MULTIPLY);
break;
case "+":
SingleCellOperation.ListDualOperations.Add(eBinaryOperationType.ADD);
break;
case "/":
SingleCellOperation.ListDualOperations.Add(eBinaryOperationType.DIVIDE);
break;
case "-":
SingleCellOperation.ListDualOperations.Add(eBinaryOperationType.SUBSTRACT);
break;
default:
return;
}
if (MainWindow.checkBoxActivePostProcess.Checked)
{
SingleCellOperation.PostProcessingOperation = new List<eBinaryOperationType>();
switch (MainWindow.domainUpDownPostProcessOperator.Text)
{
case "*":
SingleCellOperation.PostProcessingOperation.Add(eBinaryOperationType.MULTIPLY);
break;
case "+":
SingleCellOperation.PostProcessingOperation.Add(eBinaryOperationType.ADD);
break;
case "/":
SingleCellOperation.PostProcessingOperation.Add(eBinaryOperationType.DIVIDE);
break;
case "-":
SingleCellOperation.PostProcessingOperation.Add(eBinaryOperationType.SUBSTRACT);
break;
default:
return;
}
SingleCellOperation.PostProcessingValue = (double)MainWindow.numericUpDownPostProcessValue.Value;
}
foreach (cPlate CurrentPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
CurrentPlate.DBConnection.OpenConnection();
CurrentPlate.DBConnection.CreateNewColumn(NewDescType,
DescType1,
DescType2,
SingleCellOperation,
GlobalInfo, ref CurrentPlate.ListActiveWells);
CurrentPlate.DBConnection.CloseConnection();
ProgressWindow.progressBar.Value = IdxProgress++;
ProgressWindow.richTextBoxForComment.AppendText(CurrentPlate.GetShortInfo());
ProgressWindow.Refresh();
}
}
else
{
eUnaryOperationType OperationType = eUnaryOperationType.LOG;
if (MainWindow.radioButtonSQRT.Checked)
OperationType = eUnaryOperationType.SQRT;
else if (MainWindow.radioButtonLog.Checked)
OperationType = eUnaryOperationType.LOG;
else if (MainWindow.radioButtonABS.Checked)
OperationType = eUnaryOperationType.ABS;
else if (MainWindow.radioButtonEXP.Checked)
OperationType = eUnaryOperationType.EXP;
foreach (cPlate CurrentPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
CurrentPlate.DBConnection.OpenConnection();
CurrentPlate.DBConnection.CreateNewColumn(NewDescType,
DescType1,
OperationType,
GlobalInfo, ref CurrentPlate.ListActiveWells);
CurrentPlate.DBConnection.CloseConnection();
ProgressWindow.progressBar.Value = IdxProgress++;
ProgressWindow.richTextBoxForComment.AppendText(CurrentPlate.GetShortInfo());
ProgressWindow.Refresh();
}
}
ProgressWindow.Close();
int IdxNull = 0;
foreach (cPlate TmpPlate in cGlobalInfo.CurrentScreening.ListPlatesActive)
{
foreach (cWell TmpWell in TmpPlate.ListActiveWells)
if (TmpWell.ListSignatures.Count != cGlobalInfo.CurrentScreening.ListDescriptors.Count)
IdxNull++;
}
if (IdxNull > 0)
System.Windows.Forms.MessageBox.Show("List signature count is different from list descriptor count", "Critical Error !", MessageBoxButtons.OK, MessageBoxIcon.Error);
cGlobalInfo.CurrentScreening.ListDescriptors.UpDateDisplay();
// CompleteScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < cGlobalInfo.CurrentScreening.ListPlatesAvailable.Count; idxP++)
cGlobalInfo.CurrentScreening.ListPlatesActive[idxP].UpDataMinMax();
StartingUpDateUI();
this.toolStripcomboBoxPlateList.Items.Clear();
for (int IdxPlate = 0; IdxPlate < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; IdxPlate++)
{
string Name = cGlobalInfo.CurrentScreening.ListPlatesActive.GetPlate(IdxPlate).GetName();
this.toolStripcomboBoxPlateList.Items.Add(Name);
PlateListWindow.listBoxPlateNameToProcess.Items.Add(Name);
PlateListWindow.listBoxAvaliableListPlates.Items.Add(Name);
}
cGlobalInfo.CurrentScreening.CurrentDisplayPlateIdx = 0;
cGlobalInfo.CurrentScreening.SetSelectionType(comboBoxClass.SelectedIndex - 1);
UpdateUIAfterLoading();
cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().DisplayDistribution(cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptor(), false);
}
private void SubPopulationStatDescItem(object sender, EventArgs e)
{
PanelForClassSelection ClassSelectionPanel = new PanelForClassSelection(true, eClassType.PHENOTYPE);
//ClassSelectionPanel.Height = WindowToDisplay.Height;
ClassSelectionPanel.UnSelectAll();
ClassSelectionPanel.Select(0);
ClassSelectionPanel.Select(1);
ClassSelectionPanel.Location = new System.Drawing.Point(10, 10);
ClassSelectionPanel.Width = 150;
ClassSelectionPanel.Height = ClassSelectionPanel.ListCheckBoxes.Count * 25;
ClassSelectionPanel.BorderStyle = BorderStyle.Fixed3D;
FormForStatDesc NewWindow = new FormForStatDesc(this.GlobalInfo);
NewWindow.panelForSubPopulation.Controls.Add(ClassSelectionPanel);
NewWindow.textBoxDescName.Text = cGlobalInfo.CurrentScreening.ListDescriptors[IntToTransfer].GetName() + "_Average";
if (NewWindow.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
if ((NewWindow.comboBoxStatistics.Text != "Average") && (NewWindow.comboBoxStatistics.Text != "Stdev") &&
(NewWindow.comboBoxStatistics.Text != "Sum") && (NewWindow.comboBoxStatistics.Text != "Median") && (NewWindow.comboBoxStatistics.Text != "MAD") && (NewWindow.comboBoxStatistics.Text != "CV%"))
return;
List<cCellularPhenotype> LCP = new List<cCellularPhenotype>();
for (int IdxPheno = 0; IdxPheno < ClassSelectionPanel.GetListSelectedClass().Count; IdxPheno++)
{
if (ClassSelectionPanel.GetListSelectedClass()[IdxPheno])
LCP.Add(cGlobalInfo.ListCellularPhenotypes[IdxPheno]);
}
if (LCP.Count == 0) return;
double RatioPopulation = 1;
string description = "This descriptor has been generated by computing the " + NewWindow.textBoxDescName.Text + " of " + RatioPopulation * 100 + "% the following phenotypic sub-populations:\n";
foreach (var item in LCP)
{
description += item.Name + "\n";
}
cDescriptorType NewAverageType = new cDescriptorType(NewWindow.textBoxDescName.Text, true, 1, description);
cGlobalInfo.CurrentScreening.ListDescriptors.AddNew(NewAverageType);
FormForProgress ProgressWindow = new FormForProgress();
ProgressWindow.Show();
int IdxProgress = 0;
int MaxProgress = 0;
foreach (cPlate CurrentPlateToProcess in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
MaxProgress += (int)CurrentPlateToProcess.ListActiveWells.Count;
ProgressWindow.progressBar.Maximum = MaxProgress;
foreach (cPlate TmpPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
foreach (cWell Tmpwell in TmpPlate.ListActiveWells)
{
TmpPlate.DBConnection = new cDBConnection(TmpPlate, Tmpwell.SQLTableName);
List<cDescriptorType> LDT = new List<cDescriptorType>();
LDT.Add(cGlobalInfo.CurrentScreening.ListDescriptors[IntToTransfer]);
cExtendedTable CT = TmpPlate.DBConnection.GetWellValues(Tmpwell, LDT, LCP, RatioPopulation);
cListSignature LDesc = new cListSignature();
double Value = 0;
if (CT.Count == 1)
{
if (CT[0].Count == 0)
{
Value = 0;
richTextBoxConsole.AppendText(TmpPlate.GetName() + " : " + Tmpwell.GetShortInfo().Remove(Tmpwell.GetShortInfo().Length - 2) + ": no objects fullfill your request. Statistics set to null.\n");
}
else
{
if (NewWindow.comboBoxStatistics.Text == "Average")
Value = CT[0].Average();
else if (NewWindow.comboBoxStatistics.Text == "Stdev")
Value = CT[0].Std();
else if (NewWindow.comboBoxStatistics.Text == "Sum")
Value = CT[0].Sum();
else if (NewWindow.comboBoxStatistics.Text == "Median")
Value = CT[0].Median();
else if (NewWindow.comboBoxStatistics.Text == "MAD")
Value = CT[0].MAD(true);
else if (NewWindow.comboBoxStatistics.Text == "CV%")
Value = CT[0].CV();
}
}
ProgressWindow.richTextBoxForComment.AppendText(Tmpwell.GetShortInfo() + ": " + CT[0].Count.ToString() + " / " + Tmpwell.GetNumBiologicalObjects() + "\n");
cSignature NewDesc = new cSignature(Value, NewAverageType, cGlobalInfo.CurrentScreening);
LDesc.Add(NewDesc);
Tmpwell.AddSignatures(LDesc);
TmpPlate.DBConnection.CloseConnection();
ProgressWindow.progressBar.Value = IdxProgress++;
ProgressWindow.richTextBoxForComment.AppendText(TmpPlate.GetName() + " : " + Tmpwell.GetShortInfo().Remove(Tmpwell.GetShortInfo().Length - 2) + "\n");
ProgressWindow.Refresh();
}
}
ProgressWindow.Close();
cGlobalInfo.CurrentScreening.ListDescriptors.UpDateDisplay();
cGlobalInfo.CurrentScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; idxP++)
cGlobalInfo.CurrentScreening.ListPlatesActive[idxP].UpDataMinMax();
}
private void SingleCellOperationPhenotypToDesc(object sender, EventArgs e)
{
string description = "This descriptor has been generated by converting single cell phenotypic class into feature\n";
FormForNameRequest FFNR = new FormForNameRequest();
FFNR.Text = "Descriptor Name";
FFNR.textBoxForName.Text = "Phenotype Class";
if (FFNR.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
if (FFNR.textBoxForName.Text == "") return;
cDescriptorType NewDescType = new cDescriptorType(FFNR.textBoxForName.Text, true, cGlobalInfo.ListCellularPhenotypes.Count, true);
cGlobalInfo.CurrentScreening.ListDescriptors.AddNew(NewDescType);
FormForProgress ProgressWindow = new FormForProgress();
ProgressWindow.Show();
int IdxProgress = 0;
int MaxProgress = 0;
foreach (cPlate CurrentPlateToProcess in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
MaxProgress += (int)CurrentPlateToProcess.ListActiveWells.Count;
ProgressWindow.progressBar.Maximum = MaxProgress;
foreach (cPlate CurrentPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
CurrentPlate.DBConnection.OpenConnection();
CurrentPlate.DBConnection.CreateNewColumnFromExisting(NewDescType, "Phenotype_Class", GlobalInfo, ref CurrentPlate.ListActiveWells);
CurrentPlate.DBConnection.CloseConnection();
ProgressWindow.progressBar.Value = IdxProgress++;
ProgressWindow.progressBar.Refresh();
}
ProgressWindow.Close();
int IdxNull = 0;
foreach (cPlate TmpPlate in cGlobalInfo.CurrentScreening.ListPlatesActive)
{
foreach (cWell TmpWell in TmpPlate.ListActiveWells)
if (TmpWell.ListSignatures.Count != cGlobalInfo.CurrentScreening.ListDescriptors.Count)
IdxNull++;
}
if (IdxNull > 0)
System.Windows.Forms.MessageBox.Show("List signature count is different from list descriptor count", "Critical Error !", MessageBoxButtons.OK, MessageBoxIcon.Error);
cGlobalInfo.CurrentScreening.ListDescriptors.UpDateDisplay();
// CompleteScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < cGlobalInfo.CurrentScreening.ListPlatesAvailable.Count; idxP++)
cGlobalInfo.CurrentScreening.ListPlatesActive[idxP].UpDataMinMax();
StartingUpDateUI();
this.toolStripcomboBoxPlateList.Items.Clear();
for (int IdxPlate = 0; IdxPlate < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; IdxPlate++)
{
string Name = cGlobalInfo.CurrentScreening.ListPlatesActive.GetPlate(IdxPlate).GetName();
this.toolStripcomboBoxPlateList.Items.Add(Name);
PlateListWindow.listBoxPlateNameToProcess.Items.Add(Name);
PlateListWindow.listBoxAvaliableListPlates.Items.Add(Name);
}
cGlobalInfo.CurrentScreening.CurrentDisplayPlateIdx = 0;
cGlobalInfo.CurrentScreening.SetSelectionType(comboBoxClass.SelectedIndex - 1);
UpdateUIAfterLoading();
cGlobalInfo.CurrentScreening.GetCurrentDisplayPlate().DisplayDistribution(cGlobalInfo.CurrentScreening.ListDescriptors.GetActiveDescriptor(), false);
}
private void RatioPopDescItem(object sender, EventArgs e)
{
cGUI_2ClassesSelection GUI_ListClasses = new cGUI_2ClassesSelection();
GUI_ListClasses.ClassType = eClassType.PHENOTYPE;
GUI_ListClasses.PanelRight_IsCheckBoxes = true;
GUI_ListClasses.PanelLeft_IsCheckBoxes = true;
if (GUI_ListClasses.Run(this.GlobalInfo).IsSucceed == false) return;
List<cCellularPhenotype> LCP0 = new List<cCellularPhenotype>();
List<cCellularPhenotype> LCP1 = new List<cCellularPhenotype>();
for (int IdxPheno = 0; IdxPheno < GUI_ListClasses.GetOutPut()[0].Count; IdxPheno++)
{
if (GUI_ListClasses.GetOutPut()[0][IdxPheno] == 1)
LCP0.Add(cGlobalInfo.ListCellularPhenotypes[IdxPheno]);
if (GUI_ListClasses.GetOutPut()[1][IdxPheno] == 1)
LCP1.Add(cGlobalInfo.ListCellularPhenotypes[IdxPheno]);
}
//if (LCP.Count == 0) return;
string description = "Ratio of:\n";
foreach (var item in LCP0)
description += item.Name + "\n";
description += "over\n";
foreach (var item in LCP1)
description += item.Name + "\n";
cDescriptorType NewAverageType = new cDescriptorType("Ratio_Pop", true, 1, description);
cGlobalInfo.CurrentScreening.ListDescriptors.AddNew(NewAverageType);
FormForProgress ProgressWindow = new FormForProgress();
ProgressWindow.Show();
int IdxProgress = 0;
int MaxProgress = 0;
foreach (cPlate CurrentPlateToProcess in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
MaxProgress += (int)CurrentPlateToProcess.ListWells.Count;
ProgressWindow.progressBar.Maximum = MaxProgress;
foreach (cPlate TmpPlate in cGlobalInfo.CurrentScreening.ListPlatesAvailable)
{
foreach (cWell Tmpwell in TmpPlate.ListWells)
{
TmpPlate.DBConnection = new cDBConnection(TmpPlate, Tmpwell.SQLTableName);
List<cDescriptorType> LDT = new List<cDescriptorType>();
LDT.Add(cGlobalInfo.CurrentScreening.ListDescriptors[0]);
cExtendedTable CT = TmpPlate.DBConnection.GetWellValues(Tmpwell, LDT, LCP0, 1);
double NumObject0 = CT[0].Count;
cExtendedTable CT1 = TmpPlate.DBConnection.GetWellValues(Tmpwell, LDT, LCP1, 1);
double NumObject1 = CT1[0].Count;
cListSignature LDesc = new cListSignature();
double Value = 0;
if (NumObject1 == 0)
Value = 0;
else
Value = NumObject0 / NumObject1;
cSignature NewDesc = new cSignature(Value, NewAverageType, cGlobalInfo.CurrentScreening);
LDesc.Add(NewDesc);
Tmpwell.AddSignatures(LDesc);
TmpPlate.DBConnection.CloseConnection();
ProgressWindow.richTextBoxForComment.AppendText(TmpPlate.GetName() + " : " + Tmpwell.GetShortInfo().Remove(Tmpwell.GetShortInfo().Length - 2) + "\n");
ProgressWindow.progressBar.Value = IdxProgress++;
ProgressWindow.Refresh();
}
}
ProgressWindow.Close();
cGlobalInfo.CurrentScreening.ListDescriptors.UpDateDisplay();
cGlobalInfo.CurrentScreening.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < cGlobalInfo.CurrentScreening.ListPlatesActive.Count; idxP++)
cGlobalInfo.CurrentScreening.ListPlatesActive[idxP].UpDataMinMax();
}
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 void ExportToHTML(cDescriptorType Desc)
{
if (Desc.IsConnectedToDatabase == false) return;
List<cDescriptorType> LCDT = new List<cDescriptorType>();
LCDT.Add(Desc);
List<cCellularPhenotype> ListCellularPhenotypesToBeSelected = new List<cCellularPhenotype>();
cGUI_ListClasses GUIClasses = new cGUI_ListClasses();
GUIClasses.IsCheckBoxes = true;
GUIClasses.IsSelectAll = true;
GUIClasses.ClassType = eClassType.PHENOTYPE;
if (!GUIClasses.Run().IsSucceed) return;
int IDx = 0;
foreach (var item in cGlobalInfo.ListCellularPhenotypes)
{
if ((GUIClasses.GetOutPut()[0][IDx++] != 0))
ListCellularPhenotypesToBeSelected.Add(item);
}
cExtendedTable ET = new cExtendedTable(cGlobalInfo.CurrentScreening.Columns, cGlobalInfo.CurrentScreening.Rows, 0);
ET.Name = this.Name + " [" + Desc.GetName() + "]";
ET.ListRowNames = new List<string>();
for (int i = 0; i < ET[0].Count; i++)
{
ET.ListRowNames.Add(((char)(i + 65)).ToString());
}
FormForProgress MyProgressBar = new FormForProgress();
MyProgressBar.progressBar.Maximum = this.ListActiveWells.Count;
MyProgressBar.Show();
//ET.ListTags = new List<object>();
for (int i = 0; i < cGlobalInfo.CurrentScreening.Columns; i++)
{
ET[i].ListTags = new List<object>();
ET[i].Name = (i + 1).ToString();
for (int j = 0; j < cGlobalInfo.CurrentScreening.Rows; j++)
{
MyProgressBar.progressBar.Update();
cWell TmpWell = this.GetWell(i, j, true);
if (TmpWell == null)
{
ET[i].ListTags.Add("n.a.");
continue;
}
MyProgressBar.progressBar.Value++;
cExtendedTable TmpET = null;
if (cGlobalInfo.OptionsWindow.FFAllOptions.checkBoxHTMLExportStackedHisto.Checked)
TmpET = TmpWell.GetValuesList(LCDT, ListCellularPhenotypesToBeSelected, true);
else
TmpET = TmpWell.GetValuesList(LCDT, ListCellularPhenotypesToBeSelected, false);
TmpET.Name = "[" + TmpWell.GetPos() + "] - " + TmpET[0].Count + " Objects";
// get the values associated to this well and descriptor
if (cGlobalInfo.OptionsWindow.FFAllOptions.checkBoxHTMLExportStackedHisto.Checked)
{
cExtendedTable FinalTable = new cExtendedTable();
FinalTable.Name = "Stacked Histogram - " + this.GetName();
int Idx = 0;
foreach (var item in cGlobalInfo.ListCellularPhenotypes)
{
FinalTable.Add(new cExtendedList());
FinalTable[Idx].Name = item.Name;
FinalTable[Idx].Tag = item;
for (int k = 0; k < TmpET[1].Count; k++)
{
if (TmpET[1][k] == Idx)
FinalTable[Idx].Add(TmpET[0][k]);
}
Idx++;
}
cViewerStackedHistogram VSH = new cViewerStackedHistogram();
VSH.SetInputData(FinalTable);//TmpET);
VSH.Chart.LabelAxisX = Desc.GetName();
VSH.Chart.IsLine = false;
VSH.Chart.CurrentTitle.Text = TmpET.Name;
if ((cGlobalInfo.OptionsWindow.radioButtonHistoDisplayManualMinMax.Checked) || (cGlobalInfo.OptionsWindow.radioButtonHistoDisplayAutomatedMinMax.Checked))
{
VSH.Chart.DefaultAxisXMin = new cExtendedList();
VSH.Chart.DefaultAxisXMin.Add((double)cGlobalInfo.OptionsWindow.numericUpDownManualMin.Value);
VSH.Chart.DefaultAxisXMax = new cExtendedList();
VSH.Chart.DefaultAxisXMax.Add((double)cGlobalInfo.OptionsWindow.numericUpDownManualMax.Value);
if (cGlobalInfo.OptionsWindow.FFAllOptions.checkBoxHTMLExportBackColorClass.Checked)
VSH.Chart.BackgroundColor = TmpWell.GetClassColor();
}
VSH.Chart.BinNumber = Desc.GetBinNumber();
VSH.Chart.IsShadow = false;
VSH.Chart.IsBorder = false;
VSH.Run();
ET[i].ListTags.Add((Chart)VSH.Chart);
}
else
{
cViewerHistogram VH = new cViewerHistogram();
VH.SetInputData(TmpET);
VH.Chart.LabelAxisX = Desc.GetName();
VH.Chart.CurrentTitle.Text = TmpET.Name;
if ((cGlobalInfo.OptionsWindow.radioButtonHistoDisplayManualMinMax.Checked) || (cGlobalInfo.OptionsWindow.radioButtonHistoDisplayAutomatedMinMax.Checked))
{
VH.Chart.DefaultAxisXMin = new cExtendedList();
VH.Chart.DefaultAxisXMin.Add((double)cGlobalInfo.OptionsWindow.numericUpDownManualMin.Value);
VH.Chart.DefaultAxisXMax = new cExtendedList();
VH.Chart.DefaultAxisXMax.Add((double)cGlobalInfo.OptionsWindow.numericUpDownManualMax.Value);
if (cGlobalInfo.OptionsWindow.FFAllOptions.checkBoxHTMLExportBackColorClass.Checked)
VH.Chart.BackgroundColor = TmpWell.GetClassColor();
}
VH.Run();
ET[i].ListTags.Add((Chart)VH.Chart);
}
}
}
MyProgressBar.Close();
cTableToHTML TToHTML = new cTableToHTML();
TToHTML.IsDisplayUIForFilePath = true;
TToHTML.SetInputData(ET);
TToHTML.Run();
}
private void buttonStartCluster_Click(object sender, EventArgs e)
{
FormSingleCellClusteringInfo WindowClusteringInfo = new FormSingleCellClusteringInfo(GlobalInfo);
if (WindowClusteringInfo.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
Instances ListInstances = GlobalInfo.CurrentScreen.CellBasedClassification.CreateInstancesWithoutClass(dt);
if ((WindowClusteringInfo.radioButtonAutomated.Checked) && (WindowClusteringInfo.radioButtonEM.Checked))
{
ClusterEvaluation eval;
Classes = new cExtendedList();
weka.clusterers.EM EMCluster = new EM();
if(WindowClusteringInfo.checkBoxEMAutomated.Checked)
EMCluster.setNumClusters(-1);
else
EMCluster.setNumClusters((int)WindowClusteringInfo.numericUpDownClassNumber.Value);
EMCluster.buildClusterer(ListInstances);
EMCluster.getClusterModelsNumericAtts();
eval = new ClusterEvaluation();
eval.setClusterer(EMCluster);
eval.evaluateClusterer(ListInstances);
Classes.AddRange(eval.getClusterAssignments());
NumClusters= eval.getNumClusters();
ReDraw();
FormForCellByCellClusteringResults WindowFormForCellByCellClusteringResults = new FormForCellByCellClusteringResults();
WindowFormForCellByCellClusteringResults.richTextBoxResults.Clear();
WindowFormForCellByCellClusteringResults.richTextBoxResults.AppendText(eval.clusterResultsToString());
if (WindowFormForCellByCellClusteringResults.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
}
else if (WindowClusteringInfo.radioButtonDescriptorBased.Checked)
{
Classes = new cExtendedList();
DataTable FinalDataTable = new DataTable();
int IdxDescForClassSelect = WindowClusteringInfo.comboBoxDescriptorForClass.SelectedIndex;
for (int IdxWell = 0; IdxWell < GlobalInfo.ListSelectedWell.Count; IdxWell++)
{
cWell TmpWell = GlobalInfo.ListSelectedWell[IdxWell];
// if (IdxWell == 0)
if (TmpWell.ListDescriptors[IdxDescForClassSelect].GetAssociatedType().DataType == eDataType.HISTOGRAM)
{
Classes.AddRange(TmpWell.ListDescriptors[IdxDescForClassSelect].GetOriginalValues());
}
else
{
double ClasseValue = TmpWell.ListDescriptors[IdxDescForClassSelect].GetValue();
for (int IdxCell = 0; IdxCell < TmpWell.CellNumber; IdxCell++)
Classes.Add(ClasseValue);
//TmpWell.AddDescriptors
}
}
List<double> ListClassValues = new List<double>();
foreach (var item in Classes.Distinct())
{
ListClassValues.Add(item);
}
//(List<double>)Classes.Distinct();
NumClusters = ListClassValues.Count();
//Classes = new cExtendedList();
for (int IdxClust = 0; IdxClust < Classes.Count; IdxClust++)
{
for (int IdxCl = 0; IdxCl < ListClassValues.Count; IdxCl++)
{
if (ListClassValues[IdxCl] == Classes[IdxClust])
{
Classes[IdxClust] = IdxCl;
break;
}
}
//Classes[IdxClust] = ListClassValues.Find(Classes[IdxClust]);
}
//int NumClusters =
ReDraw();
}
// ReDraw();
//if (MessageBox.Show("Do you want perform a j48 training process ?", "Question", MessageBoxButtons.YesNo, MessageBoxIcon.Question) != System.Windows.Forms.DialogResult.Yes) return;
weka.core.FastVector attVals = new FastVector();
for (int i = 0; i < NumClusters; i++)
attVals.addElement("Class__" + (i).ToString());
ListInstances.insertAttributeAt(new weka.core.Attribute("Class__", attVals), ListInstances.numAttributes());
for (int i = 0; i < Classes.Count; i++)
{
ListInstances.get(i).setValue(ListInstances.numAttributes() - 1, Classes[i]);
}
ListInstances.setClassIndex(ListInstances.numAttributes() - 1);
GlobalInfo.CurrentScreen.CellBasedClassification.ClassificationModel_CellBased = new weka.classifiers.trees.J48();
GlobalInfo.CurrentScreen.CellBasedClassification.SetJ48Tree((weka.classifiers.trees.J48)GlobalInfo.CurrentScreen.CellBasedClassification.ClassificationModel_CellBased,Classes.Count);
GlobalInfo.CurrentScreen.CellBasedClassification.J48Model.setMinNumObj((int)GlobalInfo.OptionsWindow.numericUpDownJ48MinNumObjects.Value);
weka.core.Instances train = new weka.core.Instances(ListInstances, 0, ListInstances.numInstances());
GlobalInfo.CurrentScreen.CellBasedClassification.ClassificationModel_CellBased.buildClassifier(train);
GlobalInfo.ConsoleWriteLine(GlobalInfo.CurrentScreen.CellBasedClassification.ClassificationModel_CellBased.ToString());
GlobalInfo.CurrentScreen.CellBasedClassification.evaluation = new weka.classifiers.Evaluation(ListInstances);
GlobalInfo.CurrentScreen.CellBasedClassification.evaluation.crossValidateModel(GlobalInfo.CurrentScreen.CellBasedClassification.ClassificationModel_CellBased, ListInstances, 2, new java.util.Random(1));
GlobalInfo.CurrentScreen.CellBasedClassification.DisplayTree(GlobalInfo).Show();
FormForCellbyCellClassif WindowFormForCellbyCellClassif = new FormForCellbyCellClassif();
if (WindowFormForCellbyCellClassif.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
int DescrCount = GlobalInfo.CurrentScreen.ListDescriptors.Count;
// first we update the descriptor
for (int i = 0; i < ListInstances.numClasses(); i++)
GlobalInfo.CurrentScreen.ListDescriptors.AddNew(new cDescriptorsType("Ratio_Class " + i, true, 1, GlobalInfo));
FormForProgress ProgressWindow = new FormForProgress();
ProgressWindow.Show();
int IdxProgress = 0;
int MaxProgress = 0;
foreach (cPlate CurrentPlateToProcess in GlobalInfo.CurrentScreen.ListPlatesAvailable)
MaxProgress += CurrentPlateToProcess.ParentScreening.Columns * CurrentPlateToProcess.ParentScreening.Rows;
ProgressWindow.progressBar.Maximum = MaxProgress;
attVals = new FastVector();
for (int i = 0; i < NumClusters; i++)
attVals.addElement(i.ToString());
//ParallelOptions options = new ParallelOptions();
//options.MaxDegreeOfParallelism = -1; // -1 is for unlimited. 1 is for sequential.
//Stopwatch stopwatch = new Stopwatch();
//stopwatch.Start();
//////for (int PlateIdx = 0; PlateIdx < NumberOfPlates; PlateIdx++)
//int NumberOfPlates = CompleteScreening.ListPlatesAvailable.Count;
//Parallel.For(0, NumberOfPlates, options, (PlateIdx) =>
//{
// cPlate CurrentPlateToProcess = CompleteScreening.ListPlatesActive.GetPlate((string)Parent.GlobalInfo.PlateListWindow.listBoxPlateNameToProcess.Items[PlateIdx]);
// for (int row = 0; row < Parent.Rows; row++)
// for (int col = 0; col < Parent.Columns; col++)
// {
// TempWell = CurrentPlateToProcess.GetWell(col, row, false);
// if (TempWell == null) continue;
// else
// {
// if (TempWell.GetClass() == this.ClassForClassif)
// Pos.Add(TempWell.ListDescriptors[Parent.ListDescriptors.CurrentSelectedDescriptor].GetValue());
// }
// }
//}
//);
foreach (cPlate CurrentPlateToProcess in GlobalInfo.CurrentScreen.ListPlatesAvailable)
//Parallel.ForEach(GlobalInfo.CurrentScreen.ListPlatesActive, options, CurrentPlateToProcess =>
{
//Parallel.ForEach(CurrentPlateToProcess.ListActiveWells, options, TmpWell =>
for(int j=0;j<CurrentPlateToProcess.ParentScreening.Rows;j++)
for (int k = 0; k < CurrentPlateToProcess.ParentScreening.Columns; k++)
{
cWell TmpWell = CurrentPlateToProcess.GetWell(k, j, false);
if (TmpWell == null) continue;
ProgressWindow.progressBar.Value = IdxProgress++;
//DataTable FinalDataTable = new DataTable();
//TmpWell.AssociatedPlate.DBConnection = new cDBConnection(TmpWell.AssociatedPlate, TmpWell.SQLTableName);
//TmpWell.AssociatedPlate.DBConnection.AddWellToDataTable(TmpWell, FinalDataTable, false);
DataTable FinalDataTable = TmpWell.GetDescDataTable(true);
Instances ListInstancesTOClassify = GlobalInfo.CurrentScreen.CellBasedClassification.CreateInstancesWithoutClass(FinalDataTable);
ListInstancesTOClassify.insertAttributeAt(new weka.core.Attribute("Class", attVals), ListInstancesTOClassify.numAttributes());
ListInstancesTOClassify.setClassIndex(ListInstancesTOClassify.numAttributes() - 1);
cExtendedList ListClasses = new cExtendedList();
for (int i = 0; i < ListInstancesTOClassify.numInstances(); i++)
{
double classId = GlobalInfo.CurrentScreen.CellBasedClassification.ClassificationModel_CellBased.classifyInstance(ListInstancesTOClassify.instance(i));
ListClasses.Add(classId);
}
List<double[]> Histo = ListClasses.CreateHistogram(0, ListInstances.numClasses() - 1, ListInstances.numClasses() - 1);
List<cDescriptor> LDesc = new List<cDescriptor>();
for (int IdxHisto = 0; IdxHisto < Histo[1].Length; IdxHisto++)
{
double Value = (100.0 * Histo[1][IdxHisto]) / (double)ListInstancesTOClassify.numInstances();
cDescriptor NewDesc = new cDescriptor(Value, GlobalInfo.CurrentScreen.ListDescriptors[IdxHisto + DescrCount], GlobalInfo.CurrentScreen);
LDesc.Add(NewDesc);
}
TmpWell.AddDescriptors(LDesc);
//TmpWell.AssociatedPlate.DBConnection.DB_CloseConnection();
}//);
}
ProgressWindow.Close();
if (WindowFormForCellbyCellClassif.checkBoxKeepOriginalDesc.Checked == false)
{
// int DescNumToRemove = GlobalInfo.CurrentScreen.ListDescriptors.Count -
for (int IdxDesc = 0; IdxDesc < DescrCount; IdxDesc++)
GlobalInfo.CurrentScreen.ListDescriptors.RemoveDesc(GlobalInfo.CurrentScreen.ListDescriptors[0], GlobalInfo.CurrentScreen);
}
GlobalInfo.CurrentScreen.ListDescriptors.UpDateDisplay();
GlobalInfo.CurrentScreen.UpDatePlateListWithFullAvailablePlate();
for (int idxP = 0; idxP < GlobalInfo.CurrentScreen.ListPlatesActive.Count; idxP++)
GlobalInfo.CurrentScreen.ListPlatesActive[idxP].UpDataMinMax();
if (WindowFormForCellbyCellClassif.checkBoxKeepOriginalDesc.Checked == false)
GlobalInfo.CurrentScreen.GetCurrentDisplayPlate().DisplayDistribution(0, false);
//WindowFormForCellbyCellClassif.Close();
//WindowClusteringInfo.Close();
}