/// <summary>
/// Returns dictionary that contains all directories for input and output files
/// </summary>
/// <param name="dir">Input directory</param>
/// <param name="output">Output directory</param>
/// <returns></returns>
public static Dictionary <string, FileDirData> StartDigging(string dir, string output)
{
Dictionary <string, FileDirData> LinkedFiles = new Dictionary <string, FileDirData>();
List <string> files = DigForFiles(dir);
List <string> normFiles = NormalizeFileNames(files).ToList();
FileDirData curData = null;
string name, normName;
int ind = 0;
//foreach (var name in files)
for (int i = 0; i < files.Count; i++)
{
name = files[i];
normName = normFiles[i];
if (!name.EndsWith(".RoiSet"))
{
if (name.EndsWith("_Q2.tif"))
{
curData = new FileDirData(name);
}
else if (normFiles.Contains(normName.Replace(".tif", ".RoiSet")))
{
ind = normFiles.IndexOf(normName.Replace(".tif", ".RoiSet"));
curData = new FileDirData(name, files[ind]);
}
else if (normFiles.Contains(normName.Replace(".tif", "_G.RoiSet")))
{
ind = normFiles.IndexOf(normName.Replace(".tif", "_G.RoiSet"));
curData = new FileDirData(name, files[ind]);
}
else if (normFiles.Contains(normName.Replace(".tif", "_R.RoiSet")))
{
// ind = normFiles.IndexOf(normName.Replace(".tif", "_R.RoiSet"));
// curData = new FileDirData(name, files[ind]);
curData = null;
}
else
{
curData = null;
}
if (curData != null)
{
curData.ChangeOutputPath(dir, output);
LinkedFiles.Add(name, curData);
}
}
}
return(LinkedFiles);
}
/// <summary>
/// Copy the current file directory data
/// </summary>
/// <returns>New File directory data</returns>
public FileDirData Duplicate()
{
FileDirData output = new FileDirData(InputDir, InputRoi);
output.OutputDir = this._OutputDir;
output.OutputDir_CTResults = this._OutputDir_CTResults;
output.OutputDir_NormExp = this._OutputDir_NormExp;
output.OutputDir_Results = this._OutputDir_Results;
output.OutputDir_CTResults = this._OutputDir_CTResults;
output.OutputDir_Soble = this._OutputDir_Sobel;
return(output);
}
/// <summary>
/// Analyse image file - crop with tracking, copy Polygonal ROI, apply Sobel operator and save the results
/// </summary>
/// <param name="DirData">Output and input directories </param>
/// <returns>True if file successfully processed</returns>
public static bool Analyse(FileDirData DirData, double[] background)
{
TifFileInfo fi = new TifFileInfo();
// try
{
//read celltool 3 image
var console = Console.Out;
Console.SetOut(TextWriter.Null);
Console.SetError(TextWriter.Null);
fi = Cell_Tool_3.FileDecoder.ReadImage(DirData.InputDir); //read the image
Cell_Tool_3.FileDecoder.LoadRoiSet(DirData.InputRoi, fi); //read roi file
Console.SetOut(console);
Console.SetError(console);
int curInd = 1;
if (fi.roiList != null && fi.roiList[0] != null)
{
foreach (ROI roi in fi.roiList[0])
{
if (roi.Checked && roi.Type == 1 && roi.Shape > 1)
{
FileDirData curDirData = DirData.Duplicate();
if (!curDirData.InputDir.EndsWith("_CompositeRegistred.tif") &&
!curDirData.InputDir.EndsWith("_Q2.tif") &&
!curDirData.InputDir.EndsWith("_1.tif"))
{
curDirData.ExtractClipNumber();
curDirData.AddCellIndex(curInd.ToString());
}
ProcessSingleRoi(fi, roi, curDirData, background);
}
curInd++;
}
}
//clear and report
fi.Delete();
return(true);
}
//catch
{
//clear and report
fi.Delete();
return(false);
}
}
private static void ProcessSingleRoi(TifFileInfo fi, ROI roi, FileDirData dirData, double[] background)
{
if (!dirData.InputDir.EndsWith("_CompositeRegistred.tif") &&
!dirData.InputDir.EndsWith("_Q2.tif") &&
!dirData.InputDir.EndsWith("_1.tif"))
{
fi = MultiCropper.ProcessROI(dirData.OutputDir, roi, fi);
}
else
{
MultiCropper.RecalculateOriginalROI(roi, null, fi);
}
if (fi == null)
{
return;
}
fi.yAxisTB = 1;
fi.xAxisTB = 1;
fi.autoDetectBandC = true;
//Save the original image
fi.Dir = dirData.OutputDir;
if (!dirData.InputDir.EndsWith("_CompositeRegistred.tif") &&
!dirData.InputDir.EndsWith("_Q2.tif") &&
!dirData.InputDir.EndsWith("_1.tif"))
{
MultiCrop.FileEncoder.SaveTif(fi, dirData.OutputDir);
}
//Apply expression normalizer and save the image
fi.Dir = dirData.OutputDir_NormExp;
for (int c = 0; c < fi.sizeC; c++)
{
fi.cValue = c;
if (c < background.Length)
{
ExpressionNormalizer.Process(background[c], fi);
}
else
{
ExpressionNormalizer.Process(background[0], fi);
}
}
MultiCrop.FileEncoder.SaveTif(fi, dirData.OutputDir_NormExp);
//apply sobel operator
fi.Dir = dirData.OutputDir_Soble;
for (int c = 0; c < fi.sizeC; c++)
{
fi.cValue = c;
SobelOperator.applySobel(fi);
}
switch (fi.bitsPerPixel)
{
case 8:
fi.image8bit = fi.image8bitFilter;
break;
case 16:
fi.image16bit = fi.image16bitFilter;
break;
}
MultiCrop.FileEncoder.SaveTif(fi, dirData.OutputDir_Soble);
//measure results
CalculateAllRois(fi);
Cell_Tool_3.ExportTxtResults.ExportAllResults(fi);
//delete info
fi.Delete();
}
