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 importScreenDirectoryToolStripMenuItem_Click(object sender, EventArgs e)
{
var dlg1 = new Ionic.Utils.FolderBrowserDialogEx();
dlg1.Description = "Select the folder containing your files";
dlg1.ShowNewFolderButton = true;
dlg1.ShowEditBox = true;
dlg1.ShowFullPathInEditBox = true;
dlg1.RootFolder = System.Environment.SpecialFolder.Desktop;
DialogResult result = dlg1.ShowDialog();
if (result != DialogResult.OK) return;
string Path = dlg1.SelectedPath;
if (Directory.Exists(Path) == false) return;
string[] ListFiles = null;
try
{
ListFiles = Directory.GetFiles(Path, "*.csv", SearchOption.AllDirectories);
}
catch (System.Exception excep)
{
MessageBox.Show(excep.Message, "Error!", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
if (ListFiles.Length == 0)
{
MessageBox.Show("No CSV files found!", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
FormForPlateSelection FFP = new FormForPlateSelection(ListFiles,true);
if (FFP.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
string[] ListFilesForPlates = FFP.GetListPlatesSelected();
ImportFiles(ListFilesForPlates);
}
