public static void ExportAllResults(TifFileInfo fi)
{
string dir = fi.Dir.Replace(".tif", "");
//background worker
//var bgw = new BackgroundWorker();
//bgw.WorkerReportsProgress = true;
fi.available = false;
//Add event for projection here
//bgw.DoWork += new DoWorkEventHandler(delegate (Object o, DoWorkEventArgs a)
{
for (int c = 0; c < fi.sizeC; c++)
{
if (fi.roiList[c] != null && fi.roiList[c].Count != 0)
{
string dir1 = dir + "_Ch" + c + "_" +
fi.LutList[c].ToString().Replace("Color [", "").Replace("]", "") +
".txt";
string dir2 = dir + "_Ch" + c + "_" +
fi.LutList[c].ToString().Replace("Color [", "").Replace("]", "") +
"_Results.txt";
//calculate the size of the result row
int resultSize = 0;
foreach (ROI roi in fi.roiList[c])
{
if (roi.Checked == true)
{
if (roi.Results == null)
{
RoiMeasure.Measure(roi, fi, c);
}
if (roi.Shape == 0 || roi.Shape == 1)
{
resultSize += roi.Results[c].Length;
}
else if (roi.Shape == 2 || roi.Shape == 3 || roi.Shape == 4 || roi.Shape == 5)
{
resultSize += 4 + roi.Stack * 4;
}
}
}
//chart result
string val = GetResults(fi, c);
if (val != "")
{
try
{
File.WriteAllText(dir1, val);
}
catch
{
Console.Write("File is used by other program!");
//((BackgroundWorker)o).ReportProgress(1);
}
}
//standart results
if (resultSize == 0)
{
continue;
}
{
//create result matrix
double[] result;
int t = 1;
int z = 1;
int position;
string str;
double time = 0;
int timeIndex = 0;
double timeT = fi.TimeSteps[timeIndex];
try
{
if (File.Exists(dir2))
{
File.Delete(dir2);
}
}
catch
{
//((BackgroundWorker)o).ReportProgress(1);
Console.Write("File is used by other program!");
continue;
}
using (StreamWriter write = new StreamWriter(dir2))
{
//titles part
List <string> titles = new List <string>();
titles.Add("ImageN");
if (fi.sizeT > 1)
{
titles.Add("T");
}
if (fi.sizeT > 1)
{
titles.Add("T(sec.)");
}
if (fi.sizeZ > 1)
{
titles.Add("Z");
}
int roiN = 1;
foreach (ROI roi in fi.roiList[c])
{
if (roi.Checked == true && roi.Results[c] != null)
{
string com = "";
if (roi.Comment != "")
{
com = ": " + roi.Comment;
}
titles.Add("Area" + roiN.ToString() + com);
titles.Add("Mean" + roiN.ToString() + com);
titles.Add("Min" + roiN.ToString() + com);
titles.Add("Max" + roiN.ToString() + com);
if (roi.Stack > 0)
{
if (roi.Shape == 0 || roi.Shape == 1)
{
for (int n = 1; n <= roi.Stack; n++)
{
titles.Add("Area" + roiN.ToString() + "." + n.ToString() + ".LeftUp" + com);
titles.Add("Mean" + roiN.ToString() + "." + n.ToString() + ".LeftUp" + com);
titles.Add("Min" + roiN.ToString() + "." + n.ToString() + ".LeftUp" + com);
titles.Add("Max" + roiN.ToString() + "." + n.ToString() + ".LeftUp" + com);
titles.Add("Area" + roiN.ToString() + "." + n.ToString() + ".RightUp" + com);
titles.Add("Mean" + roiN.ToString() + "." + n.ToString() + ".RightUp" + com);
titles.Add("Min" + roiN.ToString() + "." + n.ToString() + ".RightUp" + com);
titles.Add("Max" + roiN.ToString() + "." + n.ToString() + ".RightUp" + com);
titles.Add("Area" + roiN.ToString() + "." + n.ToString() + ".LeftDown" + com);
titles.Add("Mean" + roiN.ToString() + "." + n.ToString() + ".LeftDown" + com);
titles.Add("Min" + roiN.ToString() + "." + n.ToString() + ".LeftDown" + com);
titles.Add("Max" + roiN.ToString() + "." + n.ToString() + ".LeftDown" + com);
titles.Add("Area" + roiN.ToString() + "." + n.ToString() + ".RightDown" + com);
titles.Add("Mean" + roiN.ToString() + "." + n.ToString() + ".RightDown" + com);
titles.Add("Min" + roiN.ToString() + "." + n.ToString() + ".RightDown" + com);
titles.Add("Max" + roiN.ToString() + "." + n.ToString() + ".RightDown" + com);
}
}
else if (roi.Shape == 2 || roi.Shape == 3 || roi.Shape == 4 || roi.Shape == 5)
{
for (int n = 1; n <= roi.Stack; n++)
{
titles.Add("Area" + roiN.ToString() + "." + n.ToString() + com);
titles.Add("Mean" + roiN.ToString() + "." + n.ToString() + com);
titles.Add("Min" + roiN.ToString() + "." + n.ToString() + com);
titles.Add("Max" + roiN.ToString() + "." + n.ToString() + com);
}
}
}
}
roiN++;
}
write.WriteLine(string.Join("\t", titles));
//calculations
for (int i = c; i < fi.imageCount; i += fi.sizeC)
{
//extract row from rois
position = 0;
result = new double[resultSize];
foreach (ROI roi in fi.roiList[c])
{
if (roi.Checked == true)
{
if (roi.Shape == 0 || roi.Shape == 1)
{
if (roi.Results[i] != null &&
roi.FromT <= t && roi.ToT >= t &&
roi.FromZ <= z && roi.ToZ >= z)
{
Array.Copy(roi.Results[i], 0, result, position, roi.Results[i].Length);
}
position += roi.Results[c].Length;
}
else if (roi.Shape == 2 || roi.Shape == 3 || roi.Shape == 4 || roi.Shape == 5)
{
if (roi.Results[i] != null &&
roi.FromT <= t && roi.ToT >= t &&
roi.FromZ <= z && roi.ToZ >= z)
{
//main roi
Array.Copy(roi.Results[i], 0, result, position, 4);
position += 4;
//layers
for (int p = 4; p < roi.Results[i].Length; p += 16)
{
Array.Copy(roi.Results[i], p, result, position, 4);
position += 4;
}
}
else
{
position += 4;
//layers
for (int p = 4; p < roi.Results[i].Length; p += 16)
{
position += 4;
}
}
}
}
}
//write the line
if (CheckArrayForValues(result))
{
str = string.Join("\t", result);
if (fi.sizeZ > 1)
{
str = z.ToString() + "\t" + str;
}
if (fi.sizeT > 1)
{
str = t.ToString() + "\t" + time.ToString() + "\t" + str;
}
str = i.ToString() + "\t" + str;
write.WriteLine(str);
}
//recalculate z and t
z += 1;
if (z > fi.sizeZ)
{
z = 1;
t += 1;
if (t > fi.sizeT)
{
t = 1;
}
if (t <= timeT)
{
time += fi.TimeSteps[timeIndex + 1];
}
else
{
timeIndex += 2;
if (timeIndex < fi.TimeSteps.Count)
{
timeT += fi.TimeSteps[timeIndex];
}
else
{
timeIndex -= 2;
timeT += fi.imageCount;
}
time += fi.TimeSteps[timeIndex + 1];
}
}
}
}
}
}
}
//((BackgroundWorker)o).ReportProgress(0);
}//);
// bgw.ProgressChanged += new ProgressChangedEventHandler(delegate (Object o, ProgressChangedEventArgs a)
{
//if (a.ProgressPercentage == 0)
{
fi.available = true;
}
//else
//{
// MessageBox.Show("File is used by other program!");
// }
}//);
//Start background worker
//IA.FileBrowser.StatusLabel.Text = "Saving results...";
//start bgw
//bgw.RunWorkerAsync();
fi.available = true;
}
private void CellToolDKtoFI(CellToolDK.TifFileInfo fi, TifFileInfo oldFI)
{
if (fi == null)
{
oldFI = null;
return;
}
TifFileInfo newFI = oldFI;
newFI.zoom = fi.zoom;
newFI.Xposition = fi.Xposition;
newFI.Yposition = fi.Yposition;
//Chart
newFI.xAxisTB = fi.xAxisTB;
newFI.yAxisTB = fi.yAxisTB;
//Tracking
newFI.tracking_MaxSize = fi.tracking_MaxSize;
newFI.tracking_MinSize = fi.tracking_MinSize;
newFI.tracking_Speed = fi.tracking_Speed;
/// <summary>
/// Segmentation
/// </summary>
//filter history
newFI.FilterHistory = fi.FilterHistory;
//controls
newFI.DataSourceInd = fi.DataSourceInd;
newFI.SegmentationProtocol = fi.SegmentationProtocol;
newFI.SegmentationCBoxIndex = fi.SegmentationCBoxIndex;
newFI.thresholdsCBoxIndex = fi.thresholdsCBoxIndex;
newFI.sumHistogramChecked = fi.sumHistogramChecked;
//spotdetector controls
newFI.SpotThresh = fi.SpotThresh;
newFI.SpotColor = fi.SpotColor;
newFI.RefSpotColor = fi.RefSpotColor;
newFI.SelectedSpotThresh = fi.SelectedSpotThresh;
newFI.typeSpotThresh = fi.typeSpotThresh;
newFI.SpotTailType = fi.SpotTailType;
newFI.spotSensitivity = fi.spotSensitivity;
//specific values
newFI.thresholds = fi.thresholds;
newFI.thresholdValues = fi.thresholdValues;
newFI.thresholdColors = fi.thresholdColors;
newFI.RefThresholdColors = fi.RefThresholdColors;
//BandC
newFI.autoDetectBandC = fi.autoDetectBandC;
newFI.applyToAllBandC = fi.applyToAllBandC;
//
newFI.selectedPictureBoxColumn = fi.selectedPictureBoxColumn;
//History
newFI.History = fi.History;
newFI.HistoryPlace = fi.HistoryPlace;
newFI.undo = fi.undo;
newFI.redo = fi.redo;
newFI.delHist = fi.delHist;
//info var
newFI.frame = fi.frame;
newFI.zValue = fi.zValue;
newFI.cValue = fi.cValue;
newFI.original = fi.original;
//Not available
newFI.loaded = fi.loaded;
newFI.available = fi.available;
newFI.selected = fi.selected;
newFI.openedImages = fi.openedImages;
//tif image
newFI.image8bit = fi.image8bit;
newFI.image16bit = fi.image16bit;
newFI.image8bitFilter = fi.image8bitFilter;
newFI.image16bitFilter = fi.image16bitFilter;
//tif tags
newFI.Dir = fi.Dir;
newFI.seriesCount = fi.seriesCount;
newFI.imageCount = fi.imageCount;
newFI.sizeX = fi.sizeX;
newFI.sizeY = fi.sizeY;
newFI.sizeZ = fi.sizeZ;
newFI.umZ = fi.umZ;
newFI.umXY = fi.umXY;
newFI.sizeC = fi.sizeC;
newFI.sizeT = fi.sizeT;
newFI.bitsPerPixel = fi.bitsPerPixel;
newFI.dimensionOrder = fi.dimensionOrder;
newFI.pixelType = fi.pixelType;
newFI.FalseColored = fi.FalseColored;
newFI.isIndexed = fi.isIndexed;
newFI.MetadataComplete = fi.MetadataComplete;
newFI.DatasetStructureDescription = fi.DatasetStructureDescription;
newFI.LutList = fi.LutList;
newFI.TimeSteps = fi.TimeSteps;
newFI.Micropoint = fi.Micropoint;
//Metadata protocol info
newFI.FileDescription = fi.FileDescription;
newFI.xCompensation = fi.xCompensation;
newFI.yCompensation = fi.yCompensation;
//properties
newFI.histogramArray = fi.histogramArray;
newFI.MinBrightness = fi.MinBrightness;
newFI.MaxBrightness = fi.MaxBrightness;
newFI.adjustedLUT = fi.adjustedLUT;
//RoiManager
newFI.roiList = new List <ROI> [fi.roiList.Length];
for (int c = 0; c < fi.roiList.Length; c++)
{
if (fi.roiList[c] != null)
{
newFI.roiList[c] = new List <ROI>();
foreach (CellToolDK.ROI roi in fi.roiList[c])
{
ROI newROI = CellToolDKtoROI(roi);
newFI.roiList[c].Add(newROI);
RoiMeasure.Measure(newROI, newFI, c, IA);
}
}
}
newFI.ROICounter = fi.ROICounter;
}
