public void Save(ImageAnalyser IA)
{
TifFileInfo tifFI = this.tifFI;
if (tifFI != null)
{
if (!tifFI.available)
{
MessageBox.Show("Image is not avaliable!\nTry again later.");
return;
}
string dir = tifFI.Dir;
//background worker
var bgw = new BackgroundWorker();
bgw.WorkerReportsProgress = true;
//Add handlers to the backgroundworker
//Reports when is finished
bgw.DoWork += new DoWorkEventHandler(delegate(Object o, DoWorkEventArgs a)
{
FileEncoder.SaveTif(tifFI, dir, IA);
//report progress
((BackgroundWorker)o).ReportProgress(0);
});
bgw.ProgressChanged += new ProgressChangedEventHandler(delegate(Object o, ProgressChangedEventArgs a)
{
if (a.ProgressPercentage == 0)
{
Saved = true;
if (tifFI != null)
{
tifFI.available = true;
}
IA.FileBrowser.StatusLabel.Text = "Ready";
}
});
//Start background worker
tifFI.available = false;
IA.FileBrowser.StatusLabel.Text = "Saving Tif Image...";
IA.EnabletrackBars(false);
bgw.RunWorkerAsync();
//continue when the sae is done
while (bgw.IsBusy)
{
Application.DoEvents(); //This call is very important if you want to have a progress bar and want to update it
//from the Progress event of the background worker.
Thread.Sleep(10); //This call waits if the loop continues making sure that the CPU time gets freed before
//re-checking.
}
IA.EnabletrackBars(true);
}
else if (ResultsExtractor != null)
{
var bgw = ResultsExtractor.FileSaver.SaveCTDataFile(
(Cell_Tool_3.ResultsExtractor.MyForm)
this.ResultsExtractor.myPanel, dir);
//continue when the sae is done
while (bgw.IsBusy)
{
Application.DoEvents(); //This call is very important if you want to have a progress bar and want to update it
//from the Progress event of the background worker.
Thread.Sleep(10); //This call waits if the loop continues making sure that the CPU time gets freed before
//re-checking.
}
}
}
private string calculateCTTagValue(TifFileInfo fi, ImageAnalyser IA)
{
List <string> vals = new List <string>();
string val = titleTB.Text + "\t" +
FiltersCB.Checked.ToString() + "\t" +
SegmentationCB.Checked.ToString() + "\t" +
SpotDetCB.Checked.ToString() + "\t" +
TrackingCB.Checked.ToString() + "\t" +
fi.sizeC + "\t" +
ChartAxisCB.Checked.ToString() + "\t" +
TimeStepCB.Checked.ToString();
vals.Add(val);
if (FiltersCB.Checked)
{
vals.Add("tracking_MaxSize->" + FileEncoder.TagValueToString(fi.tracking_MaxSize));
vals.Add("tracking_MinSize->" + FileEncoder.TagValueToString(fi.tracking_MinSize));
vals.Add("tracking_Speed->" + FileEncoder.TagValueToString(fi.tracking_Speed));
}
if (SegmentationCB.Checked)
{
vals.Add("SegmentationProtocol->" + FileEncoder.TagValueToString(fi.SegmentationProtocol));
vals.Add("SegmentationCBoxIndex->" + FileEncoder.TagValueToString(fi.SegmentationCBoxIndex));
vals.Add("thresholdsCBoxIndex->" + FileEncoder.TagValueToString(fi.thresholdsCBoxIndex));
vals.Add("RefSpotColor->" + FileEncoder.TagValueToString(fi.RefSpotColor));
vals.Add("sumHistogramChecked->" + FileEncoder.TagValueToString(fi.sumHistogramChecked));
vals.Add("thresholdColors->" + FileEncoder.TagValueToString(fi.thresholdColors));
vals.Add("RefThresholdColors->" + FileEncoder.TagValueToString(fi.RefThresholdColors));
vals.Add("thresholdValues->" + FileEncoder.TagValueToString(fi.thresholdValues));
vals.Add("thresholds->" + FileEncoder.TagValueToString(fi.thresholds));
}
if (SpotDetCB.Checked)
{
vals.Add("SelectedSpotThresh->" + FileEncoder.TagValueToString(fi.SelectedSpotThresh));
vals.Add("typeSpotThresh->" + FileEncoder.TagValueToString(fi.typeSpotThresh));
vals.Add("SpotThresh->" + FileEncoder.TagValueToString(fi.SpotThresh));
vals.Add("spotSensitivity->" + FileEncoder.TagValueToString(fi.spotSensitivity));
vals.Add("SpotColor->" + FileEncoder.TagValueToString(fi.SpotColor));
vals.Add("SpotTailType->" + string.Join("\t", fi.SpotTailType));
}
if (FiltersCB.Checked)
{
if (fi.newFilterHistory != null)
{
vals.Add("newFilters->" + FileEncoder.TagValueToString(fi.newFilterHistory));
}
//vals.Add("FilterHistory->" + FileEncoder.TagValueToString(fi.FilterHistory.ToArray()));
// if (fi.watershedList.Count!=0)
//vals.Add("watershed->" + string.Join("\n", fi.watershedList));
}
if (ChartAxisCB.Checked)
{
vals.Add("xAxisTB->" + fi.xAxisTB.ToString());
vals.Add("yAxisTB->" + fi.yAxisTB.ToString());
}
if (TimeStepCB.Checked)
{
vals.Add("TimeSteps->" + FileEncoder.TagValueToString(fi.TimeSteps));
}
return(string.Join(";\n", vals));
}
public void ApplyCT3Tags(string[] BigVals, TifFileInfo fi)
{
int ind = LibTB.SelectedIndex;
LibTB.SuspendLayout();
string[] newBigVals = new string[BigVals.Length - 1];
Array.Copy(BigVals, 1, newBigVals, 0, newBigVals.Length);
string[] vals = BigVals[0].Split(new string[] { "\t" }, StringSplitOptions.None);
titleTB.Text = vals[0];
FiltersCB.Checked = bool.Parse(vals[1]);
SegmentationCB.Checked = bool.Parse(vals[2]);
SpotDetCB.Checked = bool.Parse(vals[3]);
TrackingCB.Checked = bool.Parse(vals[4]);
int sizeC = int.Parse(vals[5]);
if (vals.Length > 6)
{
ChartAxisCB.Checked = bool.Parse(vals[6]);
}
else
{
ChartAxisCB.Checked = false;
}
if (vals.Length > 7)
{
TimeStepCB.Checked = bool.Parse(vals[7]);
}
else
{
TimeStepCB.Checked = false;
}
if (sizeC == fi.sizeC)
{
fi.available = false;
fi.watershedList.Clear();
fi.tempWatershedList.Clear();
fi.FilterHistory.Clear();
fi.image16bitFilter = fi.image16bit;
fi.image8bitFilter = fi.image8bit;
fi.newFilterHistory = null;
fi.tempNewFilterHistory = null;
//Apply settings
int[] filters = IA.TabPages.myFileDecoder.ApplyCT3Tags(newBigVals, fi);
//background worker
var bgw = new BackgroundWorker();
bgw.WorkerReportsProgress = true;
//Add event for projection here
bgw.DoWork += new DoWorkEventHandler(delegate(Object o, DoWorkEventArgs a)
{
if (fi.tempNewFilterHistory == null || fi.tempNewFilterHistory.Length != fi.sizeC)
{
fi.isBinary = new bool[fi.sizeC];
fi.tempNewFilterHistory = new List <string> [fi.sizeC];
for (int i = 0; i < fi.sizeC; i++)
{
fi.tempNewFilterHistory[i] = new List <string>();
fi.isBinary[i] = false;
}
}
if (filters != null)
{
foreach (int i in filters)
{
for (int C = 0; C < fi.sizeC; C++)
{
string str = IA.Segmentation.MyFilters.DecodeOldFilters(C, i);
fi.tempNewFilterHistory[C].Add(str);
}
}
}
if (fi.tempWatershedList != null)
{
foreach (string val in fi.tempWatershedList)
{
int C = int.Parse(val.Split(new string[] { "\t" }, StringSplitOptions.None)[0]);
fi.tempNewFilterHistory[C].Add("wshed\t" + val);
}
}
fi.tempWatershedList.Clear();
//new filters
if (fi.tempNewFilterHistory != null)
{
try
{
foreach (List <string> commands in fi.tempNewFilterHistory)
{
if (commands != null)
{
foreach (string command in commands)
{
IA.Segmentation.MyFilters.FilterFromString(command, fi);
}
}
}
fi.newFilterHistory = fi.tempNewFilterHistory;
for (int i = 0; i < fi.sizeC; i++)
{
if (fi.newFilterHistory[i] == null)
{
fi.newFilterHistory[i] = new List <string>();
}
}
fi.tempNewFilterHistory = null;
}
catch { }
}
((BackgroundWorker)o).ReportProgress(0);
});
bgw.ProgressChanged += new ProgressChangedEventHandler(delegate(Object o, ProgressChangedEventArgs a)
{
IA.ReloadImages();
fi.available = true;
IA.FileBrowser.StatusLabel.Text = "Ready";
Loading = true;
LibTB.SelectedIndex = ind;
LibTB.ResumeLayout();
Loading = false;
});
//Start background worker
IA.FileBrowser.StatusLabel.Text = "Loading settings...";
//start bgw
bgw.RunWorkerAsync();
}
else
{
MessageBox.Show("Selected settings can be applied only on image with " + sizeC + " chanels!");
}
}
private static string calculateCTTagValue(TifFileInfo fi, ImageAnalyser IA)
{
List <string> vals = new List <string>();
vals.Add("seriesCount->" + fi.seriesCount.ToString());
vals.Add("imageCount->" + fi.imageCount.ToString());
vals.Add("sizeX->" + fi.sizeX.ToString());
vals.Add("sizeY->" + fi.sizeY.ToString());
vals.Add("sizeC->" + fi.sizeC.ToString());
vals.Add("sizeZ->" + fi.sizeZ.ToString());
vals.Add("sizeT->" + fi.sizeT.ToString());
vals.Add("umXY->" + fi.umXY.ToString());
vals.Add("umZ->" + fi.umZ.ToString());
vals.Add("bitsPerPixel->" + fi.bitsPerPixel.ToString());
vals.Add("dimensionOrder->" + fi.dimensionOrder);
vals.Add("pixelType->" + fi.pixelType.ToString());
vals.Add("FalseColored->" + fi.FalseColored.ToString());
vals.Add("isIndexed->" + fi.isIndexed.ToString());
vals.Add("MetadataComplete->" + fi.MetadataComplete.ToString());
vals.Add("DatasetStructureDescription->" + fi.DatasetStructureDescription);
vals.Add("Micropoint->" + fi.Micropoint.ToString());
vals.Add("autoDetectBandC->" + fi.autoDetectBandC.ToString());
vals.Add("applyToAllBandC->" + fi.applyToAllBandC.ToString());
vals.Add("xCompensation->" + fi.xCompensation.ToString());
vals.Add("yCompensation->" + fi.yCompensation.ToString());
vals.Add("DataSourceInd->" + fi.DataSourceInd.ToString());
vals.Add("LutList->" + TagValueToString(fi.LutList));
vals.Add("TimeSteps->" + TagValueToString(fi.TimeSteps));
vals.Add("MinBrightness->" + TagValueToString(fi.MinBrightness));
vals.Add("MaxBrightness->" + TagValueToString(fi.MaxBrightness));
vals.Add("tracking_MaxSize->" + TagValueToString(fi.tracking_MaxSize));
vals.Add("tracking_MinSize->" + TagValueToString(fi.tracking_MinSize));
vals.Add("tracking_Speed->" + TagValueToString(fi.tracking_Speed));
vals.Add("SegmentationProtocol->" + TagValueToString(fi.SegmentationProtocol));
vals.Add("SegmentationCBoxIndex->" + TagValueToString(fi.SegmentationCBoxIndex));
vals.Add("thresholdsCBoxIndex->" + TagValueToString(fi.thresholdsCBoxIndex));
vals.Add("SelectedSpotThresh->" + TagValueToString(fi.SelectedSpotThresh));
vals.Add("typeSpotThresh->" + TagValueToString(fi.typeSpotThresh));
vals.Add("SpotThresh->" + TagValueToString(fi.SpotThresh));
vals.Add("spotSensitivity->" + TagValueToString(fi.spotSensitivity));
vals.Add("thresholds->" + TagValueToString(fi.thresholds));
vals.Add("SpotColor->" + TagValueToString(fi.SpotColor));
vals.Add("RefSpotColor->" + TagValueToString(fi.RefSpotColor));
vals.Add("sumHistogramChecked->" + TagValueToString(fi.sumHistogramChecked));
vals.Add("SpotTailType->" + string.Join("\t", fi.SpotTailType));
vals.Add("thresholdColors->" + TagValueToString(fi.thresholdColors));
vals.Add("RefThresholdColors->" + TagValueToString(fi.RefThresholdColors));
vals.Add("thresholdValues->" + TagValueToString(fi.thresholdValues));
vals.Add("FileDescription->" + fi.FileDescription.Replace(";", ".").Replace("->", ": "));
vals.Add("xAxisTB->" + fi.xAxisTB.ToString());
vals.Add("yAxisTB->" + fi.yAxisTB.ToString());
if (fi.yAxisTB >= 5)
{
vals.Add("yFormula->" + IA.chart.Properties.GetFunction(fi.yAxisTB).Replace(";", ""));
}
//Roi part
int c = 0;
foreach (List <ROI> roiList in fi.roiList)
{
if (roiList != null)
{
foreach (ROI roi in roiList)
{
vals.Add("roi.new->" + IA.RoiMan.roi_new(c, roi));
}
}
c++;
}
//it is important FilterHistory to be the last
//vals.Add("FilterHistory->" + TagValueToString(fi.FilterHistory.ToArray()));
//if (fi.watershedList.Count != 0)
//vals.Add("watershed->" + string.Join("\n", fi.watershedList));
if (fi.newFilterHistory != null)
{
vals.Add("newFilters->" + TagValueToString(fi.newFilterHistory));
}
return(string.Join(";\n", vals));
}
private static void SaveTif_8bitRawData(TifFileInfo fi, string fileName, ImageAnalyser IA)
{
// Register the extender callback
m_parentExtender = Tiff.SetTagExtender(TagExtender);
string value = calculateCTTagValue(fi, IA);
int numberOfPages = fi.imageCount;
int width = fi.sizeX;
int height = fi.sizeY;
int samplesPerPixel = 1;
int bitsPerSample = fi.bitsPerPixel;
//check the size of the image and start the writer
int writersCount = NumberOfTiffWriters(fi);
if (writersCount == 1)
{
using (Tiff output = Tiff.Open(fileName, "w"))
{
for (int page = 0; page < numberOfPages; page++)
{
byte[][] firstPageBuffer = fi.image8bit[page];
output.SetField(TiffTag.IMAGELENGTH, height);
output.SetField(TiffTag.IMAGEWIDTH, width);
output.SetField(TiffTag.SAMPLESPERPIXEL, samplesPerPixel);
output.SetField(TiffTag.BITSPERSAMPLE, bitsPerSample);
output.SetField(TiffTag.ORIENTATION, Orientation.TOPLEFT);
output.SetField(TiffTag.PLANARCONFIG, PlanarConfig.CONTIG);
output.SetField(TiffTag.PHOTOMETRIC, Photometric.MINISBLACK);
output.SetField(TiffTag.ROWSPERSTRIP, output.DefaultStripSize(0));
output.SetField(TiffTag.COMPRESSION, Compression.NONE);
output.SetField(TiffTag.IMAGEDESCRIPTION, ImageDetails());
// specify that it's a page within the multipage file
output.SetField(TiffTag.SUBFILETYPE, FileType.PAGE);
// specify the page number
output.SetField(TiffTag.PAGENUMBER, page, numberOfPages);
if (page == numberOfPages - 1)
{
// set the custom tag
output.SetField(TIFFTAG_CellTool_METADATA, value);
}
for (int j = 0; j < height; ++j)
{
output.WriteScanline(firstPageBuffer[j], j);
}
output.WriteDirectory();
}
}
}
else
{
string newFileName = CheckForFileChain(fileName); //Remove time chain suffix
newFileName = newFileName.Substring(0, newFileName.Length - 4); //remove .tif extension
int pageMaxPerWriter = NumberOfFramesPerPart(fi); //get maximal pages per writer
fi.Dir = FileChain_GetName(0, newFileName); //set the filename to the first file from the chain
Parallel.For(0, writersCount, (ind) =>
{
int start = ind * pageMaxPerWriter;
int stop = start + pageMaxPerWriter;
using (Tiff output = Tiff.Open(FileChain_GetName(ind, newFileName), "w"))
{
for (int page = 0; start < numberOfPages && start < stop; page++, start++)
{
byte[][] firstPageBuffer = fi.image8bit[start];
output.SetField(TiffTag.IMAGELENGTH, height);
output.SetField(TiffTag.IMAGEWIDTH, width);
output.SetField(TiffTag.SAMPLESPERPIXEL, samplesPerPixel);
output.SetField(TiffTag.BITSPERSAMPLE, bitsPerSample);
output.SetField(TiffTag.ORIENTATION, Orientation.TOPLEFT);
output.SetField(TiffTag.PLANARCONFIG, PlanarConfig.CONTIG);
output.SetField(TiffTag.PHOTOMETRIC, Photometric.MINISBLACK);
output.SetField(TiffTag.ROWSPERSTRIP, output.DefaultStripSize(0));
output.SetField(TiffTag.COMPRESSION, Compression.NONE);
output.SetField(TiffTag.IMAGEDESCRIPTION, ImageDetails());
// specify that it's a page within the multipage file
output.SetField(TiffTag.SUBFILETYPE, FileType.PAGE);
// specify the page number
output.SetField(TiffTag.PAGENUMBER, page, pageMaxPerWriter);
if (start == numberOfPages - 1 || start == stop - 1)
{
// set the custom tag
output.SetField(TIFFTAG_CellTool_METADATA, value);
}
for (int j = 0; j < height; ++j)
{
output.WriteScanline(firstPageBuffer[j], j);
}
output.WriteDirectory();
}
}
});
}
// restore previous tag extender
Tiff.SetTagExtender(m_parentExtender);
}
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;
}
public void AddYAxisTBToHistory(TifFileInfo fi)
{
fi.History.Add("Chart.YAxisType(" + fi.yAxisTB.ToString() + ")");
}
private void calculate16bitHistogram(float[] h, TifFileInfo fi, int width, int height)
{
if (fi.sumHistogramChecked[fi.cValue] == false)
{
//histogram of current frame
FrameCalculator FC = new FrameCalculator();
int frame = FC.FrameC(fi, fi.cValue);
int maxVal = ushort.MaxValue + 1;
int[] lut = new int[maxVal];
//convert information to 8 bit
int step = (int)(calculateMaxIntensity(fi, frame) / 256);
GlobalStep16Bit = step;
for (int i = 0, count = 0, val = 0; i < maxVal; i++, count++)
{
if (count >= step)
{
count = 0;
if (val < 255)
{
val++;
}
}
lut[i] = val;
}
//calculate histogram
for (int y = 0; y < height; y++)
{
for (int x = 0; x < width; x++)
{
h[lut[fi.image16bitFilter[frame][y][x]]]++;
}
}
}
else
{
//histogram of all images
int[] input = new int[(int)(fi.imageCount / fi.sizeC)];
float[][] hList = new float[input.Length][];
//check wich frames are from selected color
for (int i = 0, val = fi.cValue; i < input.Length; i++, val += fi.sizeC)
{
input[i] = val;
}
//Find absolute max intensity
ushort[] maxVals = new ushort[input.Length];
Parallel.For(0, input.Length, (i) =>
{
maxVals[i] = calculateMaxIntensity(fi, input[i]);
});
ushort max = 0;
foreach (ushort val in maxVals)
{
if (val > max)
{
max = val;
}
}
int maxVal = ushort.MaxValue + 1;
int[] lut = new int[maxVal];
//convert information to 8 bit
int step = (int)(max / 256);
GlobalStep16Bit = step;
for (int i = 0, count = 0, val = 0; i < maxVal; i++, count++)
{
if (count >= step)
{
count = 0;
if (val < 255)
{
val++;
}
}
lut[i] = val;
}
//calculate histograms for all images
Parallel.For(0, input.Length, (i) =>
{
float[] h1 = new float[NGRAY];
for (int y = 0; y < height; y++)
{
for (int x = 0; x < width; x++)
{
h[lut[fi.image16bitFilter[input[i]][y][x]]]++;
}
}
hList[i] = h1;
});
//sum histograms to one
for (int hInd = 0; hInd < hList.Length; hInd++)
{
for (int i = 0; i < NGRAY; i++)
{
h[i] += hList[hInd][i];
}
}
}
}
private void PlugIn_Load(string path)
{
TifFileInfo oldFI = null;
try
{
oldFI = IA.TabPages.TabCollections[IA.TabPages.SelectedIndex].tifFI;
}
catch { }
CellToolDK.TifFileInfo fi = FItoCellToolDK(oldFI);
var DLL = Assembly.LoadFile(path);
foreach (Type type in DLL.GetExportedTypes())
{
try
{
Transmiter e = new Transmiter();
e.Changed += new TransmiterEventHandler(delegate(object o, TransmiterEventArgs a)
{
try
{
if (fi != null && oldFI != null)
{
if (fi.sizeC != oldFI.sizeC)
{
oldFI.sizeC = fi.sizeC;
FI_reduseC(fi);
FI_reduseC(oldFI);
}
CellToolDKtoFI(fi, oldFI);
if (oldFI.sizeZ > 1)
{
IA.TabPages.zTrackBar.Refresh(oldFI.zValue + 1, 1, oldFI.sizeZ);
IA.TabPages.zTrackBar.Panel.Visible = true;
}
else
{
IA.TabPages.zTrackBar.Panel.Visible = false;
}
if (oldFI.sizeT > 1)
{
IA.TabPages.tTrackBar.Refresh(oldFI.frame + 1, 1, oldFI.sizeT);
IA.TabPages.tTrackBar.Panel.Visible = true;
}
else
{
IA.TabPages.tTrackBar.Panel.Visible = false;
}
}
}
catch { MessageBox.Show("Error with reporting back!"); }
IA.ReloadImages();
});
var c = Activator.CreateInstance(type);
try
{
type.InvokeMember("Input", BindingFlags.InvokeMethod, null, c, new object[] { fi, e });
}
catch { MessageBox.Show("Input void is not avaliable!"); }
break;
}
catch { }
}
}
public void run(TifFileInfo fi, int MLEVEL)
{
fi.thresholds[fi.cValue] = MLEVEL - 1;
if (MLEVEL < 2)
{
return;
}
//create arrays in fi
fi.thresholdValues[fi.cValue] = new int[5];
Color[] refCol = fi.RefThresholdColors[fi.cValue];
switch (fi.thresholdsCBoxIndex[fi.cValue])
{
case 1:
fi.thresholdColors[fi.cValue] = new Color[]
{ refCol[0], refCol[1], Color.Transparent, Color.Transparent, Color.Transparent };
break;
case 2:
fi.thresholdColors[fi.cValue] = new Color[]
{ refCol[0], refCol[1], refCol[2], Color.Transparent, Color.Transparent };
break;
case 3:
fi.thresholdColors[fi.cValue] = new Color[]
{ refCol[0], refCol[1], refCol[2], refCol[3], Color.Transparent };
break;
case 4:
fi.thresholdColors[fi.cValue] = new Color[]
{ refCol[0], refCol[1], refCol[2], refCol[3], refCol[4] };
break;
default:
fi.thresholdColors[fi.cValue] = new Color[]
{ Color.Transparent, Color.Transparent, Color.Transparent, Color.Transparent, Color.Transparent };
break;
}
//create variables
int[] threshold = new int[MLEVEL]; // threshold
int width = fi.sizeX;
int height = fi.sizeY;
////////////////////////////////////////////
// Build Histogram
////////////////////////////////////////////
float[] h = new float[NGRAY];
buildHistogram(h, fi, width, height);
/////////////////////////////////////////////
// Build lookup tables from h
////////////////////////////////////////////
float[][] P = new float[NGRAY][];
float[][] S = new float[NGRAY][];
float[][] H = new float[NGRAY][];
buildLookupTables(P, S, H, h);
////////////////////////////////////////////////////////
// now M level loop MLEVEL dependent term
////////////////////////////////////////////////////////
float maxSig = findMaxSigma(MLEVEL, H, threshold);
//apply to LUT
switch (fi.bitsPerPixel)
{
case 8:
for (int i = 0; i < MLEVEL; i++)
{
fi.thresholdValues[fi.cValue][i] = threshold[i];
}
break;
case 16:
for (int i = 0; i < MLEVEL; i++)
{
fi.thresholdValues[fi.cValue][i] = threshold[i] * GlobalStep16Bit;
}
break;
}
}
public OtsuSegmentation(Panel mainPanel, ImageAnalyser IA)
{
this.IA = IA;
//Core panel
panel.Dock = DockStyle.Top;
panel.BackColor = IA.FileBrowser.BackGround2Color1;
panel.ForeColor = IA.FileBrowser.ShriftColor1;
panel.Visible = false;
panel.Height = 150;
mainPanel.Controls.Add(panel);
panel.BringToFront();
#region Options
GroupBox optionGB = new GroupBox();
optionGB.Text = "Options:";
optionGB.BackColor = IA.FileBrowser.BackGround2Color1;
optionGB.ForeColor = IA.FileBrowser.ShriftColor1;
optionGB.Dock = DockStyle.Top;
optionGB.Height = 85;
panel.Controls.Add(optionGB);
optionGB.BringToFront();
Label Name = new Label();
Name.Text = "Thresholds:";
Name.Width = TextRenderer.MeasureText(Name.Text, Name.Font).Width;
Name.Location = new Point(5, 18);
optionGB.Controls.Add(Name);
Name.BringToFront();
ComboBox cb = thresholdsNumCB;
cb.Text = "0";
cb.Items.AddRange(new string[] { "0", "1", "2", "3", "4" });
cb.Width = 40;
cb.Location = new Point(80, 15);
optionGB.Controls.Add(cb);
cb.BringToFront();
cb.DropDownStyle = ComboBoxStyle.DropDownList;
cb.SelectedIndex = 0;
cb.AutoSize = false;
cb.SelectedIndexChanged += new EventHandler(delegate(object o, EventArgs e)
{
TifFileInfo fi = IA.TabPages.TabCollections[IA.TabPages.SelectedIndex].tifFI;
fi.thresholdsCBoxIndex[fi.cValue] = cb.SelectedIndex;
IA.ReloadImages();
});
CheckBox checkB = sumHistogramsCheckBox;
checkB.Text = "Use SUM histogram";
checkB.Tag = "Use SUM histogram:\nCalculates histograms for all images\nand merge them into one";
checkB.Width = 150;
checkB.Checked = true;
checkB.MouseHover += Control_MouseOver;
checkB.Location = new Point(7, 35);
optionGB.Controls.Add(checkB);
checkB.BringToFront();
checkB.CheckedChanged += new EventHandler(delegate(object o, EventArgs e)
{
TifFileInfo fi = IA.TabPages.TabCollections[IA.TabPages.SelectedIndex].tifFI;
fi.sumHistogramChecked[fi.cValue] = checkB.Checked;
if (((CheckBox)o).Focused == true)
{
IA.ReloadImages();
}
});
{
Button btn = ProcessBtn;
btn.Width = 115;
btn.FlatStyle = FlatStyle.Standard;
btn.BackColor = SystemColors.ButtonFace;
btn.ForeColor = Color.Black;
btn.Text = "Process";
btn.Location = new Point(5, 58);
optionGB.Controls.Add(btn);
btn.BringToFront();
btn.Click += new EventHandler(delegate(object o, EventArgs a)
{
int MLEVEL = thresholdsNumCB.SelectedIndex + 1;
if (IA.Segmentation.SegmentationCBox.SelectedIndex == 2)
{
IA.Segmentation.Kmeans.Start(MLEVEL);
return;
}
if (IA.Segmentation.SegmentationCBox.SelectedIndex != 1)
{
return;
}
TifFileInfo fi = IA.TabPages.TabCollections[IA.TabPages.SelectedIndex].tifFI;
if (fi.available == false)
{
MessageBox.Show("Image is not ready yet! \nTry again later.");
}
else
{
//background worker
var bgw = new BackgroundWorker();
bgw.WorkerReportsProgress = true;
bgw.DoWork += new DoWorkEventHandler(delegate(Object o1, DoWorkEventArgs a1)
{
try
{
//Segmentation event
run(fi, MLEVEL);
}
catch { }
//report progress
((BackgroundWorker)o1).ReportProgress(0);
});
bgw.ProgressChanged += new ProgressChangedEventHandler(delegate(Object o1, ProgressChangedEventArgs a1)
{
fi.available = true;
IA.FileBrowser.StatusLabel.Text = "Ready";
IA.MarkAsNotSaved();
IA.ReloadImages();
});
//Apply status
IA.FileBrowser.StatusLabel.Text = "Segmentation...";
fi.available = false;
//start bgw
bgw.RunWorkerAsync();
}
});
}
#endregion Options
#region Thresholds
GroupBox threshGB = new GroupBox();
threshGB.Text = "Thresholds:";
threshGB.BackColor = IA.FileBrowser.BackGround2Color1;
threshGB.ForeColor = IA.FileBrowser.ShriftColor1;
threshGB.Dock = DockStyle.Fill;
threshGB.Height = 50;
panel.Controls.Add(threshGB);
threshGB.BringToFront();
//Color btns
Panel colorPanel = new Panel();
colorPanel.Dock = DockStyle.Left;
colorPanel.Width = 25;
threshGB.Controls.Add(colorPanel);
Panel UpPanel = new Panel();
UpPanel.Dock = DockStyle.Top;
UpPanel.Height = 15;
threshGB.Controls.Add(UpPanel);
UpPanel.BringToFront();
for (int i = 0; i < colorBtns.Length; i++)
{
Button btn = new Button();
btn.FlatStyle = FlatStyle.Flat;
btn.FlatAppearance.BorderSize = 0;
btn.ForeColor = Color.Black;
btn.Text = "";
btn.Tag = i;
btn.Dock = DockStyle.Top;
btn.Height = 25;
colorPanel.Controls.Add(btn);
colorBtns[i] = btn;
btn.BringToFront();
btn.Visible = false;
btn.MouseDown += new MouseEventHandler(ColorBtn_Click);
btn.MouseHover += new EventHandler(delegate(object o, EventArgs a)
{
if (btn.Text == "")
{
TurnOnToolTip.SetToolTip(btn, "Color " + ((int)btn.Tag).ToString()
+ ":\nLeft click to Disable\nRight click to change color");
}
else
{
TurnOnToolTip.SetToolTip(btn, "Color " + ((int)btn.Tag).ToString()
+ " - Disabled\nLeft click to Enable");
}
});
}
//threshold track bars
for (int i = 0; i < threshTrackBars.Length; i++)
{
CTTrackBar tb = new CTTrackBar();
tb.Initialize();
tb.Panel.Dock = DockStyle.Top;
tb.BackColor(IA.FileBrowser.BackGround2Color1);
tb.ForeColor(IA.FileBrowser.ShriftColor1);
tb.Panel.Visible = false;
tb.Refresh(0, 0, 10);
tb.Name.Text = "T" + (i + 1).ToString();
tb.NamePanel.Width = 30;
threshGB.Controls.Add(tb.Panel);
threshTrackBars[i] = tb;
tb.Panel.BringToFront();
tb.Value.Changed += new ChangedValueEventHandler(delegate(Object o, ChangeValueEventArgs a)
{
TrackBar_ValueChange(a, tb);
});
}
#endregion Thresholds
}
public void loadThreshAndColorBtns(TifFileInfo fi)
{
//panel.SuspendLayout();
int threshNum = fi.thresholds[fi.cValue];
int[] vals1 = fi.thresholdValues[fi.cValue];
int min = 0;
int max = 0;
switch (fi.bitsPerPixel)
{
case 8:
max = 255; // 2^8 - 1
break;
case 16:
max = ushort.MaxValue; //16383; //2^14 - 1
break;
}
for (int i = 0; i < colorBtns.Length; i++)
{
//color btns
if (i <= threshNum & colorBtns[i].Visible == false)
{
colorBtns[i].Visible = true;
colorBtns[i].BringToFront();
}
else if (i > threshNum)
{
colorBtns[i].Visible = false;
}
Color col = fi.thresholdColors[fi.cValue][i];
if (col != Color.Transparent)
{
colorBtns[i].BackColor = col;
colorBtns[i].Text = "";
}
else
{
colorBtns[i].BackColor = Color.White;
colorBtns[i].Text = "NaN";
}
//trackBars
if (i < threshNum & i < threshTrackBars.Length)
{
if (threshTrackBars[i].Panel.Visible == false)
{
threshTrackBars[i].Panel.Visible = true;
threshTrackBars[i].Panel.BringToFront();
}
threshTrackBars[i].Refresh(vals1[i + 1], min, max);
}
else if (i >= threshNum & i < threshTrackBars.Length)
{
threshTrackBars[i].Panel.Visible = false;
}
}
//Resize Panel
if (threshNum == 0)
{
panel.Height = 85;
}
else
{
panel.Height = 105 + 25 * (threshNum + 1);
}
panel.ResumeLayout();
}
private void ColorBtn_Click(object sender, MouseEventArgs e)
{
TifFileInfo fi = IA.TabPages.TabCollections[IA.TabPages.SelectedIndex].tifFI;
Button btn = (Button)sender;
if (e.Button == MouseButtons.Left)
{
//disable/enable color
if (fi.thresholdColors[fi.cValue][(int)btn.Tag] == Color.Transparent)
{
fi.thresholdColors[fi.cValue][(int)btn.Tag] =
fi.RefThresholdColors[fi.cValue][(int)btn.Tag];
}
else
{
fi.thresholdColors[fi.cValue][(int)btn.Tag] = Color.Transparent;
}
#region apply to history
Color val = fi.RefThresholdColors[fi.cValue][(int)btn.Tag];
Color oldVal = Color.Transparent;
if (fi.thresholdColors[fi.cValue][(int)btn.Tag] == Color.Transparent)
{
val = Color.Transparent; oldVal = fi.RefThresholdColors[fi.cValue][(int)btn.Tag];
}
fi.delHist = true;
IA.delHist = true;
IA.UnDoBtn.Enabled = true;
IA.DeleteFromHistory(); fi.History.Add("segmentation.SetColor("
+ fi.cValue.ToString() + "," +
((int)btn.Tag).ToString() + "," +
ColorTranslator.ToHtml(oldVal) + ")");
fi.History.Add("segmentation.SetColor("
+ fi.cValue.ToString() + "," +
((int)btn.Tag).ToString() + "," +
ColorTranslator.ToHtml(val) + ")");
IA.UpdateUndoBtns();
IA.MarkAsNotSaved();
#endregion apply to history
IA.ReloadImages();
}
else if (e.Button == MouseButtons.Right & btn.Text == "")
{
//change color
ColorDialog colorDialog1 = new ColorDialog();
colorDialog1.AllowFullOpen = true;
colorDialog1.AnyColor = true;
colorDialog1.FullOpen = true;
colorDialog1.Color = fi.RefThresholdColors[fi.cValue][(int)btn.Tag];
//set Custom Colors
if (IA.settings.CustomColors[IA.FileBrowser.ActiveAccountIndex] != "@")
{
List <int> colorsList = new List <int>();
foreach (string j in IA.settings.CustomColors[IA.FileBrowser.ActiveAccountIndex]
.Split(new[] { "\t" }, StringSplitOptions.None))
{
colorsList.Add(int.Parse(j));
}
colorDialog1.CustomColors = colorsList.ToArray();
}
// Show the color dialog.
DialogResult result = colorDialog1.ShowDialog();
//Copy Custom Colors
int[] colors = (int[])colorDialog1.CustomColors.Clone();
string txt = "@";
if (colors.Length > 0)
{
txt = colors[0].ToString();
for (int j = 1; j < colors.Length; j++)
{
txt += "\t" + colors[j].ToString();
}
}
IA.settings.CustomColors[IA.FileBrowser.ActiveAccountIndex] = txt;
IA.settings.Save();
if (result == DialogResult.OK)
{
#region apply to history
fi.delHist = true;
IA.delHist = true;
IA.UnDoBtn.Enabled = true;
IA.DeleteFromHistory(); fi.History.Add("segmentation.SetColor("
+ fi.cValue + "," + ((int)btn.Tag).ToString() + ","
+ ColorTranslator.ToHtml(fi.thresholdColors[fi.cValue][(int)btn.Tag]) + ")");
fi.History.Add("segmentation.SetColor("
+ fi.cValue + "," + ((int)btn.Tag).ToString() + ","
+ ColorTranslator.ToHtml(colorDialog1.Color) + ")");
IA.UpdateUndoBtns();
IA.MarkAsNotSaved();
#endregion apply to history
fi.RefThresholdColors[fi.cValue][(int)btn.Tag] = colorDialog1.Color;
fi.thresholdColors[fi.cValue][(int)btn.Tag] = colorDialog1.Color;
IA.ReloadImages();
}
}
}
private void TrackBar_ValueChange(ChangeValueEventArgs e, CTTrackBar tb)
{
//variables
TifFileInfo fi = IA.TabPages.TabCollections[IA.TabPages.SelectedIndex].tifFI;
int[] vals = fi.thresholdValues[fi.cValue];
int val = int.Parse(e.Value);
int valRef = val;
//find trackbar index
int index = 0;
for (int i = 0; i < threshTrackBars.Length; i++)
{
if (threshTrackBars[i] == tb)
{
index = i; break;
}
}
//Check the avaliable min
if (index > 0)
{
if (val <= vals[index])
{
val = vals[index] + 1;
}
}
//Check the avaliable max
if (index < fi.thresholds[fi.cValue] - 1)
{
if (val >= vals[index + 2])
{
val = vals[index + 2] - 1;
}
}
//refresh if value is wrong
if (val != valRef)
{
tb.Refresh(val, tb.TrackBar1.Minimum, tb.TrackBar1.Maximum);
}
//apply changes
if (val != vals[index + 1])
{
if (tb.TrackBar1.Focused == true | tb.TextBox1.Focused == true |
tb.ApplyBtn.Focused == true)
{
#region apply to history
fi.delHist = true;
IA.delHist = true;
IA.UnDoBtn.Enabled = true;
IA.DeleteFromHistory();
fi.History.Add("segmentation.SetThreshOld("
+ fi.cValue + "," + (index + 1).ToString() + ","
+ vals[index + 1].ToString() + ")");
fi.History.Add("segmentation.SetThreshOld("
+ fi.cValue + "," + (index + 1).ToString() + ","
+ val.ToString() + ")");
IA.UpdateUndoBtns();
IA.MarkAsNotSaved();
#endregion apply to history
}
vals[index + 1] = val;
IA.ReloadImages();
}
}
private void Chart1_MouseClick(object sender, MouseEventArgs e)
{
if (e.Button != MouseButtons.Right)
{
return;
}
TifFileInfo fi = IA.TabPages.TabCollections[IA.TabPages.SelectedIndex].tifFI;
Form OptionForm = new Form();
OptionForm.FormBorderStyle = FormBorderStyle.FixedDialog;
OptionForm.Width = 200;
OptionForm.Height = 180;
OptionForm.Text = "LUT";
OptionForm.StartPosition = FormStartPosition.CenterScreen;
OptionForm.WindowState = FormWindowState.Normal;
OptionForm.BackColor = PropPanel.Body.BackColor;
//Add hot keys to main form
OptionForm.KeyPreview = true;
OptionForm.KeyDown += new KeyEventHandler(OptionForm_KeyPress);
{
Label l = new Label();
l.Text = "Color:";
l.Width = TextRenderer.MeasureText(l.Text, l.Font).Width;
l.ForeColor = Color.White;
l.Location = new Point(15, 15);
OptionForm.Controls.Add(l);
Button btn = new Button();
btn.FlatAppearance.BorderSize = 0;
btn.FlatStyle = FlatStyle.Flat;
btn.Click += new EventHandler(changeLUT);
btn.BackColor = fi.LutList[fi.cValue];
btn.Location = new Point(85, 10);
btn.Width = 75;
btn.Height = 20;
btn.KeyDown += new KeyEventHandler(OptionForm_KeyPress);
OptionForm.Controls.Add(btn);
btn.BringToFront();
}
TextBox tbMin = new TextBox();
{
Label l = new Label();
l.Text = "Minimum:";
l.Width = TextRenderer.MeasureText(l.Text, l.Font).Width;
l.ForeColor = Color.White;
l.Location = new Point(15, 45);
OptionForm.Controls.Add(l);
tbMin.Location = new Point(85, 40);
tbMin.Width = 75;
tbMin.Height = 20;
tbMin.Text = fi.MinBrightness[fi.cValue].ToString();
OptionForm.Controls.Add(tbMin);
tbMin.BringToFront();
}
TextBox tbMax = new TextBox();
{
Label l = new Label();
l.Text = "Maximum:";
l.Width = TextRenderer.MeasureText(l.Text, l.Font).Width;
l.ForeColor = Color.White;
l.Location = new Point(15, 75);
OptionForm.Controls.Add(l);
tbMax.Location = new Point(85, 70);
tbMax.Width = 75;
tbMax.Height = 20;
tbMax.Text = fi.MaxBrightness[fi.cValue].ToString();
OptionForm.Controls.Add(tbMax);
tbMax.BringToFront();
}
Button OkBtn = new Button();
OptionForm.Tag = OkBtn;
OkBtn.Text = "Apply";
OkBtn.Width = 80;
OkBtn.BackColor = SystemColors.ButtonFace;
OkBtn.Location = new Point(50, 105);
OptionForm.Controls.Add(OkBtn);
OkBtn.Click += new EventHandler(delegate(object o, EventArgs a)
{
int min = 0;
int max = 0;
try { min = int.Parse(tbMin.Text); }
catch
{
MessageBox.Show("Incorrect minimum value!");
tbMin.Focus();
return;
}
if (min < 0)
{
min = 0;
}
try { max = int.Parse(tbMax.Text); }
catch
{
MessageBox.Show("Incorrect maximum value!");
tbMax.Focus();
return;
}
if (max >= fi.histogramArray[fi.cValue].Length)
{
max = fi.histogramArray[fi.cValue].Length - 1;
//IA.MarkAsNotSaved();
}
if (min > max)
{
MessageBox.Show("Minimum must be lower then the maximum!");
return;
}
if (min != fi.MinBrightness[fi.cValue] | max != fi.MaxBrightness[fi.cValue])
{
//turn of auto
if (autoDetect.Checked != false)
{
autoDetect.Checked = false;
fi.autoDetectBandC = false;
applyToAll.Visible = true;
}
//adjust brightness
MinPrew = fi.MinBrightness[fi.cValue];
MaxPrew = fi.MaxBrightness[fi.cValue];
adjustBrightness(min, max, fi, -1);
applyToHistory(fi.cValue, min, max);
//IA.MarkAsNotSaved();
//Load array to Chart
loadHistogramArray(fi);
}
OptionForm.Close();
});
OptionForm.ShowDialog();
foreach (Button btn in fi.tpTaskbar.ColorBtnList)
{
btn.Focus();
}
}
private void FI_reduseC(TifFileInfo fi)
{
List <Color> l = new List <Color>();
for (int i = 0; i < fi.sizeC; i++)
{
if (i < fi.LutList.Count)
{
l.Add(fi.LutList[i]);
}
else
{
l.Add(System.Drawing.Color.White);
}
}
fi.LutList = l;
fi.cValue = 0;
#region Segmentation variables
fi.histogramArray = null;
fi.adjustedLUT = null;
fi.MaxBrightness = null;
fi.MinBrightness = null;
fi.SegmentationCBoxIndex = new int[fi.sizeC];
fi.SegmentationProtocol = new int[fi.sizeC];
fi.thresholdsCBoxIndex = new int[fi.sizeC];
fi.sumHistogramChecked = new bool[fi.sizeC];
fi.thresholdValues = new int[fi.sizeC][];
fi.thresholdColors = new Color[fi.sizeC][];
fi.RefThresholdColors = new Color[fi.sizeC][];
fi.thresholds = new int[fi.sizeC];
fi.SpotColor = new Color[fi.sizeC];
fi.RefSpotColor = new Color[fi.sizeC];
fi.SelectedSpotThresh = new int[fi.sizeC];
fi.SpotThresh = new int[fi.sizeC];
fi.typeSpotThresh = new int[fi.sizeC];
fi.SpotTailType = new string[fi.sizeC];
fi.spotSensitivity = new int[fi.sizeC];
fi.roiList = new List <ROI> [fi.sizeC];
fi.tracking_MaxSize = new int[fi.sizeC];
fi.tracking_MinSize = new int[fi.sizeC];
fi.tracking_Speed = new int[fi.sizeC];
for (int i = 0; i < fi.sizeC; i++)
{
fi.sumHistogramChecked[i] = false;
fi.thresholdValues[i] = new int[5];
fi.thresholdColors[i] = new Color[]
{ Color.Transparent, Color.Transparent, Color.Transparent, Color.Transparent, Color.Transparent };
fi.RefThresholdColors[i] = new Color[]
{ Color.Black, Color.Orange, Color.Green, Color.Blue, Color.Magenta };
fi.SpotColor[i] = Color.Red;
fi.RefSpotColor[i] = Color.Red;
fi.SpotTailType[i] = "<";
fi.spotSensitivity[i] = 100;
fi.tracking_MaxSize[i] = 10000;
fi.tracking_MinSize[i] = 5;
fi.tracking_Speed[i] = 5;
}
#endregion Segmentation variables
fi.tpTaskbar.AddColorBtn();
fi.tpTaskbar.VisualizeColorBtns();
}
private void Chart1_MouseMove(object sender, MouseEventArgs e)
{
try
{
TifFileInfo oldFI = IA.TabPages.TabCollections[IA.TabPages.SelectedIndex].tifFI;
if (oldFI.histogramArray == null)
{
return;
}
if (moveMin == true)
{
//higher then max
int MineX = e.X;
int maxeX = Convert.ToInt32(Chart1.CA.ValueToPixelPosition(oldFI.MaxBrightness[oldFI.cValue]) - 1);
if (e.X > maxeX)
{
MineX = maxeX;
}
//lower then min
if (MineX < 0)
{
MineX = 0;
}
int newMin = Convert.ToInt32(Chart1.CA.PixelPositionToValue(MineX));
//calculate
if (newMin != oldFI.MinBrightness[oldFI.cValue] & newMin < oldFI.MaxBrightness[oldFI.cValue] & newMin >= 0)
{
if (autoDetect.Checked != false)
{
autoDetect.Checked = false;
oldFI.autoDetectBandC = false;
applyToAll.Visible = true;
}
oldFI.MinBrightness[oldFI.cValue] = newMin;
// IA.MarkAsNotSaved();
Chart1_MouseMoveImageReload();
}
}
else if (moveMax == true)
{
//calculate abs max
int absMax = 254;
TifFileInfo fi = IA.TabPages.TabCollections[IA.TabPages.SelectedIndex].tifFI;
if (fi == null)
{
return;
}
if (fi.bitsPerPixel != 8)
{
absMax = ushort.MaxValue;
}
//bigger then max
int maxeX = Convert.ToInt32(Chart1.CA.Width);
if (e.X < maxeX)
{
maxeX = e.X;
}
//lower then min
int mineX = Convert.ToInt32(Chart1.CA.ValueToPixelPosition(oldFI.MinBrightness[oldFI.cValue])) + 1;
if (e.X < mineX)
{
maxeX = mineX;
}
int newMax = Convert.ToInt32(Chart1.CA.PixelPositionToValue(maxeX));
//calculate max
if (newMax != oldFI.MaxBrightness[oldFI.cValue] & newMax > oldFI.MinBrightness[oldFI.cValue] & newMax <= absMax)
{
if (autoDetect.Checked != false)
{
autoDetect.Checked = false;
oldFI.autoDetectBandC = false;
applyToAll.Visible = true;
}
oldFI.MaxBrightness[oldFI.cValue] = newMax;
Chart1_MouseMoveImageReload();
}
}
else
{
double min = Chart1.CA.ValueToPixelPosition(lastMin);
double max = Chart1.CA.ValueToPixelPosition(lastMax);
if ((e.X > min - 2 & e.X < min + 2) | (e.X > max - 2 & e.X < max + 2))
{
Chart1.Cursor = Cursors.SizeWE;
}
else
{
Chart1.Cursor = Cursors.Default;
}
}
}
catch { }
}
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;
}
public static string GetResults(TifFileInfo fi, int c)
{
string val = "";
List <double[]> data = new List <double[]>();
#region Calculate Original Data Set
int ind, row, fromT, toT, fromZ, toZ,
t, z, position, stack, boolStart;
double[] mainRoi;
List <string> RoiNames = new List <string>()
{
"Time(s)"
};
List <string> Comments = new List <string>()
{
"Comments"
};
ROI roi;
List <int> factorsT = new List <int>();
List <int> factorsZ = new List <int>();
if (data == null)
{
data = new List <double[]>();
}
if (fi.roiList[c] != null)
{
data.Clear();
for (ind = 0; ind < fi.roiList[c].Count; ind++)
{
roi = fi.roiList[c][ind];
if (roi.Results == null || roi.Checked == false)
{
continue;
}
fromT = roi.FromT;
toT = roi.ToT;
fromZ = roi.FromZ;
toZ = roi.ToZ;
//main roi part
t = 1;
z = 1;
if (true)
{
mainRoi = new double[roi.Results.Length];
for (row = c; row < roi.Results.Length; row += fi.sizeC)
{
if (roi.Results[row] != null &&
t >= fromT && t <= toT && z >= fromZ && z <= toZ)
{
if (fi.yAxisTB == 4)
{
mainRoi[row] = roi.Results[row][0] * roi.Results[row][1];
}
else
{
mainRoi[row] = roi.Results[row][fi.yAxisTB];
}
}
//apply change t and z
z++;
if (z > fi.sizeZ)
{
z = 1;
t++;
if (t > fi.sizeT)
{
t = 1;
}
}
}
factorsT.Add(toT - fromT + 1);
factorsZ.Add(toZ - fromZ + 1);
data.Add(mainRoi);
RoiNames.Add(" Mean_ROI" + (ind + 1).ToString());
Comments.Add(roi.Comment);
}
//layers
if (roi.Stack == 0)
{
continue;
}
if (fi.yAxisTB > 4)
{
continue;
}
position = 4;
for (stack = 0; stack < roi.Stack; stack++)
{
t = 1;
z = 1;
mainRoi = new double[roi.Results.Length];
int factor = 0;
if (roi.Shape == 0 || roi.Shape == 1)
{
for (boolStart = 1 + stack * 4; boolStart < 5 + stack * 4; boolStart++, position += 4)
{
if (roi.ChartUseIndex[boolStart] == true)
{
for (row = c; row < roi.Results.Length; row += fi.sizeC)
{
if (roi.Results[row] != null &&
t >= fromT && t <= toT && z >= fromZ && z <= toZ)
{
if (fi.yAxisTB == 4)
{
mainRoi[row] += roi.Results[row][position] * roi.Results[row][position + 1];
}
else if (fi.yAxisTB < 2)
{
mainRoi[row] += roi.Results[row][position + fi.yAxisTB];
}
else if (fi.yAxisTB == 2 && (mainRoi[row] == 0 || mainRoi[row] > roi.Results[row][position + fi.yAxisTB]))
{
mainRoi[row] = roi.Results[row][position + fi.yAxisTB];
}
else if (fi.yAxisTB == 3 && mainRoi[row] < roi.Results[row][position + fi.yAxisTB])
{
mainRoi[row] = roi.Results[row][position + fi.yAxisTB];
}
}
//apply change t and z
z++;
if (z > fi.sizeZ)
{
z = 1;
t++;
if (t > fi.sizeT)
{
t = 1;
}
}
}
factor++;
}
}
}
else
{
boolStart = 1 + stack * 4;
if (roi.ChartUseIndex[boolStart] == true)
{
for (row = c; row < roi.Results.Length; row += fi.sizeC)
{
if (roi.Results[row] != null &&
t >= fromT && t <= toT && z >= fromZ && z <= toZ)
{
if (fi.yAxisTB == 4)
{
mainRoi[row] = roi.Results[row][position] * roi.Results[row][position + 1];
}
else if (fi.yAxisTB < 2)
{
mainRoi[row] = roi.Results[row][position + fi.yAxisTB];
}
else if (fi.yAxisTB == 2)
{
mainRoi[row] = roi.Results[row][position + fi.yAxisTB];
}
else if (fi.yAxisTB == 3)
{
mainRoi[row] = roi.Results[row][position + fi.yAxisTB];
}
}
//apply change t and z
z++;
if (z > fi.sizeZ)
{
z = 1;
t++;
if (t > fi.sizeT)
{
t = 1;
}
}
}
factor++;
}
position += 16;
}
if (fi.yAxisTB == 1)
{
for (int i = 0; i < mainRoi.Length; i++)
{
if (mainRoi[i] != 0)
{
mainRoi[i] /= factor;
}
}
}
factorsT.Add(toT - fromT + 1);
factorsZ.Add(toZ - fromZ + 1);
data.Add(mainRoi);
RoiNames.Add(" Mean_ROI" + (ind + 1).ToString() + ".Layer" + (stack + 1).ToString());
Comments.Add(roi.Comment);
}
}
var XaxisData = new double[fi.imageCount];
t = 1;
z = 1;
double time = 0;
int timeIndex = 0;
double timeT = fi.TimeSteps[timeIndex];
for (row = c; row < fi.imageCount; row += fi.sizeC)
{
switch (fi.xAxisTB)
{
case 0:
//T slice
XaxisData[row] = t;
break;
case 1:
//T sec
XaxisData[row] = time;
break;
case 2:
//Z slice
XaxisData[row] = z;
break;
case 3:
//T sec
XaxisData[row] = time / 60;
break;
case 4:
//T sec
XaxisData[row] = time / 3600;
break;
}
//apply change t and z
z++;
if (z > fi.sizeZ)
{
z = 1;
t++;
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];
}
}
}
#endregion Calculate Original Data Set
#region recalculate original data set
if (fi.xAxisTB < 2 || fi.xAxisTB == 3 || fi.xAxisTB == 4)
{
double[] res;
int counter;
for (ind = 0; ind < data.Count; ind++)
{
res = new double[fi.sizeT];
counter = 0;
t = 1;
z = 1;
for (row = c; row < fi.imageCount; row += fi.sizeC)
{
z++;
if (fi.yAxisTB < 2)
{
res[counter] += data[ind][row];
}
else if (fi.yAxisTB == 2 && (res[counter] > data[ind][row] || res[counter] == 0))
{
res[counter] = data[ind][row];
}
else if (fi.yAxisTB == 3 && res[counter] < data[ind][row])
{
res[counter] = data[ind][row];
}
else
{
res[counter] += data[ind][row];
}
if (z > fi.sizeZ)
{
z = 1;
t++;
if (fi.yAxisTB == 1)
{
res[counter] /= factorsZ[ind];
}
counter++;
}
}
data[ind] = res;
}
//x axis
res = new double[fi.sizeT];
counter = 0;
t = 1;
z = 1;
for (row = c; row < fi.imageCount; row += fi.sizeC)
{
z++;
if (z > fi.sizeZ)
{
z = 1;
t++;
res[counter] = XaxisData[row];
counter++;
}
}
XaxisData = res;
}
else if (fi.xAxisTB == 2)
{
double[] res;
int counter;
for (ind = 0; ind < data.Count; ind++)
{
res = new double[fi.sizeZ];
counter = 0;
t = 1;
z = 1;
for (row = c; row < fi.imageCount; row += fi.sizeC)
{
z++;
if (fi.yAxisTB < 2)
{
res[counter] += data[ind][row];
}
else if (fi.yAxisTB == 2 && (res[counter] > data[ind][row] || res[counter] == 0))
{
res[counter] = data[ind][row];
}
else if (fi.yAxisTB == 3 && res[counter] < data[ind][row])
{
res[counter] = data[ind][row];
}
else
{
res[counter] += data[ind][row];
}
counter++;
if (z > fi.sizeZ)
{
z = 1;
counter = 0;
t++;
}
}
//popravi tuk s faktor list w gornata chast
if (fi.yAxisTB == 1)
{
for (int i = 0; i < res.Length; i++)
{
res[i] /= factorsT[ind];
}
}
data[ind] = res;
}
//x axis
res = new double[fi.sizeZ];
counter = 0;
t = 1;
z = 1;
for (row = c; row < fi.imageCount; row += fi.sizeC)
{
res[counter] = XaxisData[row];
counter++;
z++;
if (z > fi.sizeZ)
{
break;
}
}
XaxisData = res;
}
#endregion recalculate original data set
//System.IO.File.WriteAllText(fi.Dir.Replace(".tif", "_c" + c + ".text"),MeargeResult());
#region Prepare string
string[] resList = new string[XaxisData.Length + 3];
//system description row
string[] temp = new string[RoiNames.Count];
temp[0] = "CTResults: Mean";
temp[1] = fi.Dir;
resList[0] = string.Join("\t", temp);
temp = null;
//comments
resList[1] = string.Join("\t", Comments);
Comments = null;
//titles
resList[2] = string.Join("\t", RoiNames);
RoiNames = null;
for (int i = 0; i < XaxisData.Length; i++)
{
val = XaxisData[i].ToString();
foreach (double[] dList in data)
{
val += "\t" + dList[i];
}
resList[i + 3] = val;
}
XaxisData = null;
data = null;
val = string.Join("\n", resList);
resList = null;
#endregion Prepare string
}
return(val);
}
private void ErrorCheck(object sender, EventArgs e)
{
TifFileInfo fi = null;
try
{
fi = IA.TabPages.TabCollections[IA.TabPages.SelectedIndex].tifFI;
}
catch { }
if (fi == null)
{
MessageBox.Show("There is no opened image!");
return;
}
if (fi.loaded == false)
{
return;
}
if (fi.roiList == null)
{
return;
}
if (nameCBox.Items.Count == 0)
{
return;
}
try
{
int c, ind;
ROI roi;
List <string> res = new List <string>();
IA.chart.Properties.Ncalc.LoadFunction(fi, nameCBox.SelectedIndex);
for (c = 0; c < fi.sizeC; c++)
{
if (fi.tpTaskbar.ColorBtnList[c].ImageIndex == 0 && fi.roiList[c] != null)
{
for (ind = 0; ind < fi.roiList[c].Count; ind++)
{
roi = fi.roiList[c][ind];
if (roi.Results == null || roi.Checked == false)
{
continue;
}
if (roi.ChartUseIndex[0] == true)
{
string val = IA.chart.Properties.Ncalc.ErrorCheck(c, roi, fi.roiList[c], fi);
if (val != "")
{
res.Add(val);
}
}
}
}
}
res.Add("Check finished!");
MessageBox.Show(string.Join("\n", res));
}
catch (Exception)
{
throw;
}
}
