public static void SaveTif(TifFileInfo fi, string dir, ImageAnalyser IA)
{
try {
//return;
//Save pixel data
switch (fi.bitsPerPixel)
{
case 8:
SaveTif_8bitRawData(fi, dir, IA);
break;
case 16:
SaveTif_16bitRawData(fi, dir, IA);
break;
default:
return;
}
//save metadata
//string value = calculateCTTagValue(fi,IA);
//image.SetField(TIFFTAG_CellTool_METADATA, value);
//AddTag(dir, value);
}
catch
{
System.Windows.Forms.MessageBox.Show("Save file error!");
}
}
public PlugInEngine(ToolStripMenuItem DeveloperToolStripMenuItem, ImageAnalyser IA)
{
this.DeveloperToolStripMenuItem = DeveloperToolStripMenuItem;
this.IA = IA;
PlugIns_TakeNames();
}
private static void SaveTif_16bitRawData1(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;
using (Tiff output = Tiff.Open(fileName, "w"))
{
for (int page = 0; page < numberOfPages; page++)
{
ushort[][] image = fi.image16bit[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 i = 0; i < height; i++)
{
ushort[] samples = image[i];
byte[] buffer = new byte[samples.Length * sizeof(ushort)];
Buffer.BlockCopy(samples, 0, buffer, 0, buffer.Length);
output.WriteScanline(buffer, i);
}
output.WriteDirectory();
}
}
// restore previous tag extender
Tiff.SetTagExtender(m_parentExtender);
}
public CTChart_Properties(Panel propertiesPanel, Panel PropertiesBody, ImageAnalyser IA)
{
this.IA = IA;
Ncalc = new Ncalc_Adapter(IA);
PropPanel = new PropertiesPanel_Item();
PropPanel_Initialize(propertiesPanel, PropertiesBody);
//GLControl event
//IA.GLControl1.MouseDown += GLControl_MouseClick_tracking;
}
public CTChart_Series(Panel propertiesPanel, Panel PropertiesBody, ImageAnalyser IA)
{
this.IA = IA;
PropPanel = new PropertiesPanel_Item();
PropPanel_Initialize(propertiesPanel, PropertiesBody);
string[] colMatrix = new string[] { "blue", "red", "#00b300", "#b300b3", "#00bfff", "#ffcc00", "#ff471a", "#cc6699", "#39e600"
, "#00b3b3", "#ffcc66", "#7575a3", "#ff1a1a", "#ff0055", "#8a00e6", "#bf8040",
"#53c68c", "#ace600", "#b33c00", "#ff6666" };
tv.ImageList = new ImageList();
tv.ImageList.ImageSize = new Size(20, 16);
foreach (string val in colMatrix)
{
RefColors.Add(ColorTranslator.FromHtml(val));
createImagesFortTV(ColorTranslator.FromHtml(val));
}
}
private TifFileInfo FindFI(ImageAnalyser IA)
{
TifFileInfo fi = null;
try
{
fi = IA.TabPages.TabCollections[IA.TabPages.SelectedIndex].tifFI;
}
catch { return(null); }
if (fi == null)
{
return(null);
}
if (fi.available == false)
{
return(null);
}
return(fi);
}
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)
{
//check is the directory exist
if (dir.IndexOf("\\") > -1)
{
string checkDir = dir.Substring(0, dir.LastIndexOf("\\"));
checkDir = OSStringConverter.StringToDir(checkDir);
if (!System.IO.Directory.Exists(checkDir))
{
System.IO.Directory.CreateDirectory(checkDir);
}
}
//save file
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)
{
//check is the directory exist
if (dir.IndexOf("\\") > -1)
{
string checkDir = dir.Substring(0, dir.LastIndexOf("\\"));
checkDir = OSStringConverter.StringToDir(checkDir);
if (!System.IO.Directory.Exists(checkDir))
{
System.IO.Directory.CreateDirectory(checkDir);
}
}
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.
}
}
}
public AutoApplySettingsClass(Button startBtn, ComboBox LibTB, ImageAnalyser IA)
{
this.startBtn = startBtn;
this.LibTB = LibTB;
this.IA = IA;
Form dialog = this;
dialog.FormBorderStyle = FormBorderStyle.FixedDialog;
dialog.Text = "Auto Settings";
dialog.StartPosition = FormStartPosition.CenterScreen;
dialog.WindowState = FormWindowState.Normal;
dialog.BackColor = IA.FileBrowser.BackGround2Color1;
dialog.ForeColor = IA.FileBrowser.ShriftColor1;
dialog.MinimizeBox = false;
dialog.MaximizeBox = false;
dialog.Width = 250;
dialog.Height = 335;
#region Add controls
this.SuspendLayout();
//ApplyToNewImage checkbox
ApplyToNewCheckB.Text = "Apply settings when new image is opened";
ApplyToNewCheckB.Location = new System.Drawing.Point(5, 5);
ApplyToNewCheckB.Width = 250;
this.Controls.Add(ApplyToNewCheckB);
ApplyToNewCheckB.CheckedChanged += ApplyToNewCheckB_Checked;
//Title
Label titleLabel = new Label();
titleLabel.Text = "Name:";
titleLabel.Width = 50;
titleLabel.Location = new System.Drawing.Point(5, 30);
this.Controls.Add(titleLabel);
//Title
titleTB.Text = "";
titleTB.Width = 165;
titleTB.Location = new System.Drawing.Point(55, 28);
this.Controls.Add(titleTB);
//GroupBox
GroupBox GB = new GroupBox();
GB.Text = "Apply the following setiings:";
GB.ForeColor = System.Drawing.Color.White;
GB.Dock = DockStyle.Bottom;
GB.Height = 200;
this.Controls.Add(GB);
CheckBox CB = FiltersCB;
{
CB.Text = "Filters";
CB.Location = new System.Drawing.Point(30, 20);
CB.ForeColor = System.Drawing.Color.White;
GB.Controls.Add(CB);
}
CB = SegmentationCB;
{
CB.Text = "Segmentation";
CB.Location = new System.Drawing.Point(30, 50);
CB.ForeColor = System.Drawing.Color.White;
GB.Controls.Add(CB);
}
CB = SpotDetCB;
{
CB.Text = "Spot detector";
CB.Location = new System.Drawing.Point(30, 80);
CB.ForeColor = System.Drawing.Color.White;
GB.Controls.Add(CB);
}
CB = TrackingCB;
{
CB.Text = "Tracking";
CB.Location = new System.Drawing.Point(30, 110);
CB.ForeColor = System.Drawing.Color.White;
GB.Controls.Add(CB);
}
CB = ChartAxisCB;
{
CB.Text = "Chart Axis";
CB.Location = new System.Drawing.Point(30, 140);
CB.ForeColor = System.Drawing.Color.White;
GB.Controls.Add(CB);
}
CB = TimeStepCB;
{
CB.Text = "Time Intervals";
CB.Location = new System.Drawing.Point(30, 170);
CB.ForeColor = System.Drawing.Color.White;
GB.Controls.Add(CB);
}
//EndPanel
Panel endP = new Panel();
endP.Dock = DockStyle.Bottom;
endP.Height = 40;
this.Controls.Add(endP);
Button EditBtn = new Button();
Button btn = EditBtn;
{
btn.Text = "Save";
btn.ForeColor = System.Drawing.Color.Black;
btn.BackColor = System.Drawing.SystemColors.ButtonFace;
btn.Width = 55;
btn.Location = new System.Drawing.Point(10, 5);
endP.Controls.Add(btn);
btn.Click += EditBtn_Click;
}
Button SaveBtn = new Button();
btn = SaveBtn;
{
btn.Text = "Save As";
btn.ForeColor = System.Drawing.Color.Black;
btn.BackColor = System.Drawing.SystemColors.ButtonFace;
btn.Width = 55;
btn.Location = new System.Drawing.Point(65, 5);
endP.Controls.Add(btn);
btn.Click += SaveBtn_Click;
}
Button DeleteBtn = new Button();
btn = DeleteBtn;
{
btn.Text = "Delete";
btn.ForeColor = System.Drawing.Color.Black;
btn.BackColor = System.Drawing.SystemColors.ButtonFace;
btn.Width = 55;
btn.Location = new System.Drawing.Point(120, 5);
endP.Controls.Add(btn);
btn.Click += deleteBtn_Click;
}
Button CancelBtn = new Button();
btn = CancelBtn;
{
btn.Text = "Cancel";
btn.ForeColor = System.Drawing.Color.Black;
btn.BackColor = System.Drawing.SystemColors.ButtonFace;
btn.Width = 55;
btn.Location = new System.Drawing.Point(175, 5);
endP.Controls.Add(btn);
btn.Click += cancelBtn_Click;
}
this.ResumeLayout();
#endregion Add controls
startBtn.Click += startBtn_Click;
this.FormClosing += Form_Clossing;
LibTB.SelectedIndexChanged += LibTB_SelectedIndexChanged;
}
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 static bool OpenFile(List <TabPage> Collection, string path, TabPage tp, ImageAnalyser IA, ToolStripStatusLabel StatusLabel)
{
StatusLabel.Text = "Reading Metadata...";
// read metadata using ImageReader
loci.formats.ImageReader FirstReader = new loci.formats.ImageReader();
try
{
FirstReader.setId(OSStringConverter.StringToDir(path));
}
catch
{
FirstReader.close();
StatusLabel.Text = "Ready";
return(false);
}
bool isRGB = FirstReader.isRGB();
//check is it rgb colored
loci.formats.ChannelSeparator reader = loci.formats.ChannelSeparator.makeChannelSeparator(FirstReader);
FirstReader = null;
TifFileInfo fi = tp.tifFI;
fi.seriesCount = reader.getSeriesCount();
//Select which series to open!!!!!
int ser = SelectSeries(reader, IA.TabPages.FileBrowser.StatusLabel);
if (ser == -1)
{
fi = null;
reader.close();
StatusLabel.Text = "Ready";
return(false);
}
else
{
reader.setSeries(ser);
}
//Check file bits per pixel - currently supported: 8 bit GrayScale, 16 bit GrayScale
fi.bitsPerPixel = reader.getBitsPerPixel();
if (fi.bitsPerPixel <= 8)
{
fi.bitsPerPixel = 8;
}
else if (fi.bitsPerPixel <= 16)
{
fi.bitsPerPixel = 16;
}
else
{
fi = null;
reader.close();
StatusLabel.Text = "Ready";
return(false);
}
//Check is the metadata complieted and return message if not
/*
* if (reader.isMetadataComplete() == false)
* {
* MessageBox.Show("Metadata is not complete!");
* }
*/
//read tags
fi.imageCount = reader.getImageCount();
fi.sizeX = reader.getSizeX();
fi.sizeY = reader.getSizeY();
fi.sizeZ = reader.getSizeZ();
fi.sizeC = reader.getSizeC();
fi.sizeT = reader.getSizeT();
//fi.dimensionOrder = reader.getDimensionOrder();
fi.dimensionOrder = "XYCZT";
fi.umZ = 0;
fi.umXY = 0;
fi.pixelType = reader.getPixelType();
fi.FalseColored = reader.isFalseColor();
fi.isIndexed = reader.isIndexed();
fi.MetadataComplete = reader.isMetadataComplete();
fi.DatasetStructureDescription = reader.getDatasetStructureDescription();
string description = getLibTifFileDescription(path);
fi.FileDescription = string.Join("\n", new string[] { "-----------------", "CoreMetadata:\n", reader.getCoreMetadataList().ToString(),
"-----------------", "GlobalMetadata:\n", reader.getGlobalMetadata().ToString(),
"-----------------", "SeriesMetadata:\n", reader.getSeriesMetadata().ToString(),
"-----------------", "FileDescription:\n", description });
//Apply def settings
fi.Dir = path;
fi.xAxisTB = IA.chart.Properties.xAxisTB.SelectedIndex;
fi.yAxisTB = IA.chart.Properties.yAxisTB.SelectedIndex;
fi.available = false;
fi.original = false;
//Create LUT table
if (isRGB)
{
fi.LutList = new List <Color>()
{
Color.FromArgb(255, 255, 0, 0),
Color.FromArgb(255, 0, 255, 0),
Color.FromArgb(255, 0, 0, 255)
};
}
else
{
fi.LutList = new List <Color>();
for (int i = 0; i < fi.sizeC; i++)
{
fi.LutList.Add(Color.White);
}
}
//Create time steps table
fi.TimeSteps = new List <double>();
fi.TimeSteps.Add(fi.imageCount + 1);
fi.TimeSteps.Add(1);
//If its IQ3 format or Dragonflye - try to read the colors and the timesteps
TryAndorDecoders(fi, description);
if (fi.sizeC == 0)
{
fi.sizeC = 1;
}
if (fi.sizeZ == 0)
{
fi.sizeZ = 1;
}
if (fi.sizeT == 0)
{
fi.sizeT = 1;
}
#region Segmentation variables
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
//background worker
var bgw = new BackgroundWorker();
bgw.WorkerReportsProgress = true;
bool loaded = false;
//Add handlers to the backgroundworker
bgw.DoWork += new DoWorkEventHandler(delegate(Object o, DoWorkEventArgs a)
{
//prepare array and read file
if (isLibTifCompatible(path) && !isRGB)
{
int[] dimOrder = GetFrameIndexes(reader, fi);
Tiff image = Tiff.Open(OSStringConverter.StringToDir(path), "r");
//prepare array and read file
int midFrame = fi.sizeC * fi.sizeZ;
switch (fi.bitsPerPixel)
{
case 8:
fi.image8bit = new byte[image.NumberOfDirectories()][][];
for (int i = 0; i < midFrame; i++)
{
if (i >= fi.imageCount)
{
break;
}
IA.TabPages.myFileDecoder.Image8bit_readFrame(i, image, fi, dimOrder);
}
break;
case 16:
fi.image16bit = new ushort[image.NumberOfDirectories()][][];
for (int i = 0; i < midFrame; i++)
{
if (i >= fi.imageCount)
{
break;
}
IA.TabPages.myFileDecoder.Image16bit_readFrame(i, image, fi, dimOrder);
}
break;
}
loaded = true;
//report progress
((BackgroundWorker)o).ReportProgress(0);
//parallel readers
IA.TabPages.myFileDecoder.ImageReader_BGW(Collection, image, fi, IA, path, dimOrder);
//report progress
dimOrder = null;
image.Close();
((BackgroundWorker)o).ReportProgress(1);
}
else
{
//Read the first T
byte[] buf;
switch (fi.bitsPerPixel)
{
case 8:
fi.image8bit = new byte[fi.imageCount][][];
buf = new byte[fi.sizeX * fi.sizeY];
for (int z = 0, i = 0; z < fi.sizeZ; z++)
{
for (int c = 0; c < fi.sizeC; c++, i++)
{
fi.image8bit[i] = Image8bit_readFrame(
reader.openBytes(
reader.getIndex(z, c, 0), buf),
fi.sizeX, fi.sizeY);
//fi.LutList[c] = ReadLut(reader);
}
}
break;
case 16:
fi.image16bit = new ushort[fi.imageCount][][];
buf = new byte[fi.sizeX * fi.sizeY * 2];
for (int z = 0, i = 0; z < fi.sizeZ; z++)
{
for (int c = 0; c < fi.sizeC; c++, i++)
{
fi.image16bit[i] = Image16bit_readFrame(
reader.openBytes(
reader.getIndex(z, c, 0), buf),
fi.sizeX, fi.sizeY);
//fi.LutList[c] = ReadLut(reader);
}
}
break;
}
loaded = true;
//report progress
((BackgroundWorker)o).ReportProgress(0);
//Read the rest T
byte[][] bigBuf = new byte[fi.imageCount][];
int ZCcount = fi.sizeC * fi.sizeZ;
for (int t = 1, i = ZCcount; t < fi.sizeT; t++)
{
for (int z = 0; z < fi.sizeZ; z++)
{
for (int c = 0; c < fi.sizeC; c++, i++)
{
if (fi.image8bit != null || fi.image16bit != null)
{
bigBuf[i] = reader.openBytes(reader.getIndex(z, c, t));
}
}
}
}
//Format the arrays for CellTool
Parallel.For(ZCcount, fi.imageCount, (int i) =>
{
try
{
switch (fi.bitsPerPixel)
{
case 8:
if (fi.image8bit != null)
{
fi.image8bit[i] = Image8bit_readFrame(bigBuf[i],
fi.sizeX, fi.sizeY);
}
bigBuf[i] = null;
break;
case 16:
if (fi.image16bit != null)
{
fi.image16bit[i] = Image16bit_readFrame(bigBuf[i],
fi.sizeX, fi.sizeY);
}
bigBuf[i] = null;
break;
}
}
catch { }
});
bigBuf = null;
//report progress
((BackgroundWorker)o).ReportProgress(1);
}
});
bgw.ProgressChanged += new ProgressChangedEventHandler(delegate(Object o, ProgressChangedEventArgs a)
{
if (a.ProgressPercentage == 0)
{
fi.openedImages = fi.sizeC * fi.sizeZ;
try
{
IA.ReloadImages();
}
catch { }
}
else if (a.ProgressPercentage == 1)
{
//dispose the reader
reader.close();
reader = null;
//mark as loaded
fi.openedImages = fi.imageCount;
fi.available = true;
fi.loaded = true;
IA.TabPages.myFileDecoder.CalculateAllRois(fi);
IA.ReloadImages();
bool check = true;
foreach (TabPage tp1 in Collection)
{
if (tp1.tifFI != null && tp1.tifFI.available == false)
{
check = false;
break;
}
}
if (check == true)
{
IA.TabPages.myFileDecoder.loadingTimer.Stop();
StatusLabel.Text = "Ready";
}
if (IA.Segmentation.AutoSetUp.LibTB.SelectedIndex > 0 &&
IA.Segmentation.AutoSetUp.ApplyToNewCheckB.Checked &&
MessageBox.Show("Do you want to open the image with the following protocol:\n" +
IA.Segmentation.AutoSetUp.LibTB.Text,
"", MessageBoxButtons.YesNo) == System.Windows.Forms.DialogResult.Yes)
{
IA.Segmentation.AutoSetUp.ApplyCT3Tags(IA.Segmentation.AutoSetUp.protocols[
IA.Segmentation.AutoSetUp.LibTB.SelectedIndex].Split(
new string[] { ";\n" }, StringSplitOptions.None), fi);
}
}
});
//Start background worker
StatusLabel.Text = "Reading Image...";
//Clear OldImage
IA.IDrawer.ClearImage();
//start bgw
bgw.RunWorkerAsync();
//add taskbar
tp.tifFI.tpTaskbar.Initialize(IA.TabPages.ImageMainPanel, IA, fi);
try
{
if (loaded == true)
{
IA.ReloadImages();
}
}
catch { }
//out put
return(true);
}
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);
}
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 loci.formats.ChannelSeparator ReadMetadata(string path, List <TabPage> Collection, TabPage tp, ImageAnalyser IA)
{
// read metadata using ImageReader
loci.formats.ImageReader FirstReader = new loci.formats.ImageReader();
try
{
FirstReader.setId(path);
}
catch
{
FirstReader.close();
IA.FileBrowser.StatusLabel.Text = "Ready";
return(null);
}
bool isRGB = FirstReader.isRGB();
//check is it rgb colored
loci.formats.ChannelSeparator reader = loci.formats.ChannelSeparator.makeChannelSeparator(FirstReader);
FirstReader = null;
TifFileInfo fi = tp.tifFI;
fi.seriesCount = reader.getSeriesCount();
//Select which series to open!!!!!
int ser = SelectSeries(reader);
if (ser == -1)
{
fi = null;
reader.close();
IA.FileBrowser.StatusLabel.Text = "Ready";
return(null);
}
else
{
reader.setSeries(ser);
}
//Check file bits per pixel - currently supported: 8 bit GrayScale, 16 bit GrayScale
fi.bitsPerPixel = reader.getBitsPerPixel();
if (fi.bitsPerPixel <= 8)
{
fi.bitsPerPixel = 8;
}
else if (fi.bitsPerPixel <= 16)
{
fi.bitsPerPixel = 16;
}
else
{
fi = null;
reader.close();
IA.FileBrowser.StatusLabel.Text = "Ready";
return(null);
}
//Check is the metadata complieted and return message if not
/*
* if (reader.isMetadataComplete() == false)
* {
* MessageBox.Show("Metadata is not complete!");
* }
*/
//read tags
fi.imageCount = reader.getImageCount();
fi.sizeX = reader.getSizeX();
fi.sizeY = reader.getSizeY();
fi.sizeZ = reader.getSizeZ();
fi.sizeC = reader.getSizeC();
fi.sizeT = reader.getSizeT();
//fi.dimensionOrder = reader.getDimensionOrder();
fi.dimensionOrder = "XYCZT";
fi.umZ = 0;
fi.umXY = 0;
fi.pixelType = reader.getPixelType();
fi.FalseColored = reader.isFalseColor();
fi.isIndexed = reader.isIndexed();
fi.MetadataComplete = reader.isMetadataComplete();
fi.DatasetStructureDescription = reader.getDatasetStructureDescription();
string description = getLibTifFileDescription(path);
fi.FileDescription = string.Join("\n", new string[] { "-----------------", "CoreMetadata:\n", reader.getCoreMetadataList().ToString(),
"-----------------", "GlobalMetadata:\n", reader.getGlobalMetadata().ToString(),
"-----------------", "SeriesMetadata:\n", reader.getSeriesMetadata().ToString(),
"-----------------", "FileDescription:\n", description });
//Apply def settings
fi.Dir = path;
fi.xAxisTB = IA.chart.Properties.xAxisTB.SelectedIndex;
fi.yAxisTB = IA.chart.Properties.yAxisTB.SelectedIndex;
fi.available = false;
fi.original = false;
//Create LUT table
if (isRGB)
{
fi.LutList = new List <Color>()
{
Color.FromArgb(255, 255, 0, 0),
Color.FromArgb(255, 0, 255, 0),
Color.FromArgb(255, 0, 0, 255)
};
}
else
{
fi.LutList = new List <Color>();
for (int i = 0; i < fi.sizeC; i++)
{
fi.LutList.Add(Color.White);
}
}
//Create time steps table
fi.TimeSteps = new List <double>();
fi.TimeSteps.Add(fi.imageCount + 1);
fi.TimeSteps.Add(1);
//If its IQ3 format or Dragonflye - try to read the colors and the timesteps
TryAndorDecoders(fi, description);
if (fi.sizeC == 0)
{
fi.sizeC = 1;
}
if (fi.sizeZ == 0)
{
fi.sizeZ = 1;
}
if (fi.sizeT == 0)
{
fi.sizeT = 1;
}
#region Segmentation variables
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
return(reader);
}
/// <summary>
/// Initializes this class
/// </summary>
private void Awake()
{
// Allows this instance to behave like a singleton
Instance = this;
}
public void Initialize(Panel MainPanel, ImageAnalyser IA1, TifFileInfo tifFI1)
{
tifFI = tifFI1;
IA = IA1;
int w = 30;
int h = 30;
TopBar.Width = MainPanel.Width - w;
TopBar.Height = h;
TopBar.Dock = DockStyle.Top;
//MainPanel.Controls.Add(TopBar);
IA.IDrawer.corePanel.Height = TopBar.Height;
IA.IDrawer.corePanel.Controls.Add(TopBar);
TopBar.BringToFront();
ColorPanel.Dock = DockStyle.Right;
ColorPanel.BackColor = IA.FileBrowser.BackGround2Color1;
TopBar.Controls.Add(ColorPanel);
ColorPanel.BringToFront();
XYValPanel.Controls.Add(XLabel);
XLabel.Font = new Font(XLabel.Font.Name, 6.9F);
XLabel.Location = new Point(0, 15);
XLabel.Text = "X: 10000";
XLabel.Visible = false;
XLabel.Width = 45;
XYValPanel.Controls.Add(YLabel);
YLabel.Font = new Font(XLabel.Font.Name, 6.9F);
YLabel.Location = new Point(47, 15);
YLabel.Text = "Y: 10000";
YLabel.Visible = false;
YLabel.Width = 45;
XYValPanel.Controls.Add(ValLabel);
ValLabel.Font = new Font(XLabel.Font.Name, 6.9F);
ValLabel.Location = new Point(94, 15);
ValLabel.Text = "Value: 10000";
ValLabel.Width = 70;
ValLabel.Visible = false;
XYValPanel.Dock = DockStyle.Right;
XYValPanel.Width = 165;
XYValPanel.BackColor = IA.FileBrowser.BackGroundColor1;
TopBar.Controls.Add(XYValPanel);
XYValPanel.BringToFront();
Panel SmallColorPanel = new Panel();
SmallColorPanel.BackColor = IA.FileBrowser.BackGroundColor1;
SmallColorPanel.Dock = DockStyle.Top;
SmallColorPanel.Height = 5;
ColorPanel.Controls.Add(SmallColorPanel);
MethodsPanel.Dock = DockStyle.Left;
MethodsPanel.BackColor = IA.FileBrowser.BackGroundColor1;
MethodsPanel.Width = 100;
TopBar.Controls.Add(MethodsPanel);
MethodsPanel.BringToFront();
Refresh();
VisualizeColorBtns();
VisualizeMethodsBtns();
}
public MyWatershed(ImageAnalyser IA)
{
this.IA = IA;
createDialog();
}
public CTChart(ImageAnalyser IA)
{
this.IA = IA;
}
public KMeansSegmentation(ImageAnalyser IA)
{
this.IA = IA;
}
private static bool SubstackToolStripMenuItem_click(string path, List <TabPage> Collection, TabPage tp, ImageAnalyser IA, loci.formats.ChannelSeparator reader, int[][] dim)
{
TifFileInfo fi = tp.tifFI;
if (dim == null)
{
return(false);
}
////////
/////background worker
bool loaded = false;
//Add handlers to the backgroundworker
var bgw = new BackgroundWorker();
bgw.WorkerReportsProgress = true;
TifFileInfo newFI = null;
//Add event for projection here
bgw.DoWork += new DoWorkEventHandler(delegate(Object o, DoWorkEventArgs a)
{
//Prepare matrix
int T, Z, C, f = 0,
curT, curZ, curC;
List <int> matrix = new List <int>();
for (T = 0, curT = dim[0][0] - 1; T < fi.sizeT; T++)
{
if (T == curT && T < dim[0][1])
{
for (Z = 0, curZ = dim[1][0] - 1; Z < fi.sizeZ; Z++)
{
if (Z == curZ && Z < dim[1][1])
{
for (C = 0, curC = dim[2][0] - 1; C < fi.sizeC; C++, f++)
{
if (C == curC && C < dim[2][1])
{
//matrix.Add(f);
matrix.Add(reader.getIndex(Z, C, T));
curC += dim[2][2];
}
}
curZ += dim[1][2];
}
else
{
f += fi.sizeC;
}
}
curT += dim[0][2];
}
else
{
f += fi.sizeC * fi.sizeZ;
}
}
newFI = fi;
newFI.Dir = newFI.Dir.Substring(0, newFI.Dir.LastIndexOf(".")) +
"_Substack.tif";
newFI.sizeT = 0;
for (int i = dim[0][0] - 1; i < dim[0][1]; i += dim[0][2])
{
newFI.sizeT++;
}
newFI.sizeZ = 0;
for (int i = dim[1][0] - 1; i < dim[1][1]; i += dim[1][2])
{
newFI.sizeZ++;
}
newFI.sizeC = 0;
List <Color> colList = new List <Color>();
for (int i = dim[2][0] - 1; i < dim[2][1]; i += dim[2][2])
{
newFI.sizeC++;
colList.Add(fi.LutList[i]);
}
newFI.imageCount = matrix.Count;
newFI.openedImages = matrix.Count;
AddEmptyArraysToFI(newFI);
newFI.LutList = colList;
//read image
//Read the first T
//prepare array and read file
if (isLibTifCompatible(path) && !reader.isRGB())
{
int[] dimOrder = matrix.ToArray();
Tiff image = Tiff.Open(path, "r");
//prepare array and read file
int midFrame = fi.sizeC * fi.sizeZ;
switch (fi.bitsPerPixel)
{
case 8:
fi.image8bit = new byte[fi.imageCount][][];
for (int i = 0; i < midFrame; i++)
{
if (i >= fi.imageCount)
{
break;
}
IA.TabPages.myFileDecoder.Image8bit_readFrame(i, image, fi, dimOrder);
}
break;
case 16:
fi.image16bit = new ushort[fi.imageCount][][];
for (int i = 0; i < midFrame; i++)
{
if (i >= fi.imageCount)
{
break;
}
IA.TabPages.myFileDecoder.Image16bit_readFrame(i, image, fi, dimOrder);
}
break;
}
loaded = true;
//report progress
((BackgroundWorker)o).ReportProgress(0);
//parallel readers
IA.TabPages.myFileDecoder.ImageReader_BGW(Collection, image, fi, IA, path, dimOrder);
//report progress
dimOrder = null;
image.Close();
((BackgroundWorker)o).ReportProgress(1);
}
else
{
byte[] buf;
switch (fi.bitsPerPixel)
{
case 8:
fi.image8bit = new byte[fi.imageCount][][];
buf = new byte[fi.sizeX * fi.sizeY];
for (int z = 0, i = 0; z < fi.sizeZ; z++)
{
for (int c = 0; c < fi.sizeC; c++, i++)
{
fi.image8bit[i] = Image8bit_readFrame(
reader.openBytes(
matrix[i], buf),
fi.sizeX, fi.sizeY);
//fi.LutList[c] = ReadLut(reader);
}
}
break;
case 16:
fi.image16bit = new ushort[fi.imageCount][][];
buf = new byte[fi.sizeX * fi.sizeY * 2];
for (int z = 0, i = 0; z < fi.sizeZ; z++)
{
for (int c = 0; c < fi.sizeC; c++, i++)
{
fi.image16bit[i] = Image16bit_readFrame(
reader.openBytes(
matrix[i], buf),
fi.sizeX, fi.sizeY);
//fi.LutList[c] = ReadLut(reader);
}
}
break;
}
loaded = true;
//report progress
((BackgroundWorker)o).ReportProgress(0);
//Read the rest T
byte[][] bigBuf = new byte[fi.imageCount][];
int ZCcount = fi.sizeC * fi.sizeZ;
for (int t = 1, i = ZCcount; t < fi.sizeT; t++)
{
for (int z = 0; z < fi.sizeZ; z++)
{
for (int c = 0; c < fi.sizeC; c++, i++)
{
if (fi.image8bit != null || fi.image16bit != null)
{
bigBuf[i] = reader.openBytes(matrix[i]);
}
}
}
}
//Format the arrays for CellTool
Parallel.For(ZCcount, fi.imageCount, (int i) =>
{
try
{
switch (fi.bitsPerPixel)
{
case 8:
if (fi.image8bit != null)
{
fi.image8bit[i] = Image8bit_readFrame(bigBuf[i],
fi.sizeX, fi.sizeY);
}
bigBuf[i] = null;
break;
case 16:
if (fi.image16bit != null)
{
fi.image16bit[i] = Image16bit_readFrame(bigBuf[i],
fi.sizeX, fi.sizeY);
}
bigBuf[i] = null;
break;
}
}
catch { }
});
bigBuf = null;
//report progress
((BackgroundWorker)o).ReportProgress(1);
}
});
bgw.ProgressChanged += new ProgressChangedEventHandler(delegate(Object o, ProgressChangedEventArgs a)
{
if (a.ProgressPercentage == 0)
{
fi.openedImages = fi.sizeC * fi.sizeZ;
try
{
IA.ReloadImages();
}
catch { }
}
else if (a.ProgressPercentage == 1)
{
//dispose the reader
reader.close();
reader = null;
//mark as loaded
fi.openedImages = fi.imageCount;
fi.available = true;
fi.loaded = true;
newFI.original = false;
IA.TabPages.myFileDecoder.CalculateAllRois(fi);
IA.ReloadImages();
bool check = true;
foreach (TabPage tp1 in Collection)
{
if (tp1.tifFI != null && tp1.tifFI.available == false)
{
check = false;
break;
}
}
if (check == true)
{
IA.TabPages.myFileDecoder.loadingTimer.Stop();
IA.FileBrowser.StatusLabel.Text = "Ready";
}
if (IA.Segmentation.AutoSetUp.LibTB.SelectedIndex > 0 &&
IA.Segmentation.AutoSetUp.ApplyToNewCheckB.Checked &&
MessageBox.Show("Do you want to open the image with the following protocol:\n" +
IA.Segmentation.AutoSetUp.LibTB.Text,
"", MessageBoxButtons.YesNo) == System.Windows.Forms.DialogResult.Yes)
{
IA.Segmentation.AutoSetUp.ApplyCT3Tags(IA.Segmentation.AutoSetUp.protocols[
IA.Segmentation.AutoSetUp.LibTB.SelectedIndex].Split(
new string[] { ";\n" }, StringSplitOptions.None), fi);
}
}
});
//Start background worker
IA.FileBrowser.StatusLabel.Text = "Reading Image...";
//Clear OldImage
IA.IDrawer.ClearImage();
//start bgw
bgw.RunWorkerAsync();
//add taskbar
tp.tifFI.tpTaskbar.Initialize(IA.TabPages.ImageMainPanel, IA, fi);
try
{
if (loaded == true)
{
IA.ReloadImages();
}
}
catch { }
//output
return(true);
}
/// <summary>
/// Check the file size and if there is no avaliable RAM - open only a fragment of the image
/// </summary>
/// <param name="path"></param>
/// <param name="Collection"></param>
/// <param name="tp"></param>
/// <param name="IA1"></param>
/// <returns></returns>
public static bool OpenBigImage(string path, List <TabPage> Collection, TabPage tp, ImageAnalyser IA)
{
//Check the file size in bytes
long FileSize = new System.IO.FileInfo(path).Length;
//Check the free ram memory in bytes
long RAM = (long)new ComputerInfo().AvailablePhysicalMemory;
// RAM = 10000000;
if (FileSize < RAM)
{
return(false);
}
else
{
loci.formats.ChannelSeparator reader;
//read file metadata
try
{
reader = ReadMetadata(path, Collection, tp, IA);
}
catch
{
MessageBox.Show("Error: Not avaliable file format!");
IA.FileBrowser.StatusLabel.Text = "Ready";
return(false);
}
if (reader == null)
{
MessageBox.Show("Error: Not avaliable file format!");
IA.FileBrowser.StatusLabel.Text = "Ready";
return(false);
}
//get new file dimentions
int[][] matrix = null;
while (!CheckSize(RAM, matrix, tp.tifFI))
{
matrix = SubstackDialog(tp.tifFI);
if (matrix == null)
{
reader.close();
reader = null;
IA.FileBrowser.StatusLabel.Text = "Ready";
return(false);
}
}
return(SubstackToolStripMenuItem_click(path, Collection, tp, IA, reader, matrix));
}
}
public Ncalc_Adapter(ImageAnalyser IA)
{
this.IA = IA;
}
public SpotDetector(Panel mainPanel, ImageAnalyser IA)
{
this.IA = IA;
Panel p1 = new Panel();
p1.Height = 5;
p1.Dock = DockStyle.Top;
mainPanel.Controls.Add(p1);
p1.BringToFront();
#region Threshold
{
CTTrackBar tb = new CTTrackBar();
tb.Initialize();
tb.Panel.Dock = DockStyle.Top;
tb.BackColor(IA.FileBrowser.BackGround2Color1);
tb.ForeColor(IA.FileBrowser.ShriftColor1);
tb.Panel.Visible = true;
tb.Refresh(0, 0, 10);
tb.Name.Text = "Threshold:";
tb.NamePanel.Width = 62;
mainPanel.Controls.Add(tb.Panel);
thresh = tb;
tb.Panel.BringToFront();
tb.Value.Changed += new ChangedValueEventHandler(delegate(Object o, ChangeValueEventArgs a)
{
thresh_valueChange(int.Parse(a.Value));
});
}
#endregion Threshold
#region Options
{
CTTrackBar tb = new CTTrackBar();
tb.Initialize();
tb.Panel.Dock = DockStyle.Top;
tb.BackColor(IA.FileBrowser.BackGround2Color1);
tb.ForeColor(IA.FileBrowser.ShriftColor1);
tb.Panel.Visible = true;
tb.Refresh(100, 1, 100);
tb.Name.Text = "Sensitivity:";
tb.NamePanel.Width = 62;
mainPanel.Controls.Add(tb.Panel);
sensitivity = tb;
tb.Panel.BringToFront();
tb.Value.Changed += new ChangedValueEventHandler(delegate(Object o, ChangeValueEventArgs a)
{
sensitivity_valueChange(int.Parse(a.Value));
});
}
Panel p = new Panel();
p.Height = 30;
p.Dock = DockStyle.Top;
mainPanel.Controls.Add(p);
p.BringToFront();
//Thresh list box
selectT.Tag = "Select Threshold";
selectT.Width = 60;
selectT.Location = new Point(53, 1);
selectT.Items.Add("None");
selectT.DropDownStyle = ComboBoxStyle.DropDownList;
selectT.SelectedIndex = 0;
selectT.AutoSize = false;
p.Controls.Add(selectT);
selectT.BringToFront();
selectT.MouseHover += Control_MouseOver;
selectT.SelectedIndexChanged += selectT_IndexChange;
//ThreshType box
tType.Tag = "Set threshold type";
tType.Width = 60;
tType.Location = new Point(120, 1);
tType.Items.AddRange(new string[] { "Pixels", "% Max" });
tType.DropDownStyle = ComboBoxStyle.DropDownList;
tType.SelectedIndex = 0;
tType.AutoSize = false;
p.Controls.Add(tType);
tType.BringToFront();
tType.MouseHover += Control_MouseOver;
tType.SelectedIndexChanged += TType_IndexChange;
//Color btn
{
Button btn = new Button();
ColBtn = btn;
btn.FlatStyle = FlatStyle.Flat;
btn.FlatAppearance.BorderSize = 0;
btn.BackColor = Color.Red;
btn.ForeColor = Color.Black;
btn.Location = new Point(3, 1);
btn.Text = "";
btn.Tag = "Select color for the spots";
btn.Height = 22;
btn.Width = 25;
p.Controls.Add(btn);
btn.BringToFront();
btn.Visible = true;
btn.MouseHover += Control_MouseOver;
btn.MouseDown += ColBtn_Click;
}
//<>btn
{
Button btn = new Button();
TailType = btn;
btn.FlatStyle = FlatStyle.Flat;
btn.FlatAppearance.BorderSize = 0;
btn.ForeColor = Color.White;
btn.Location = new Point(28, 1);
btn.Text = ">";
btn.Tag = "Set spot intensity diapason";
btn.Height = 22;
btn.Width = 25;
p.Controls.Add(btn);
btn.BringToFront();
btn.Visible = true;
btn.MouseHover += Control_MouseOver;
btn.Click += TailType_Click;
}
#endregion Options
}
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
}
private int xmin; //of selection created
#endregion CellTool variables
/** Constructs a Wand object from an ImageProcessor. */
public Wand(ImageAnalyser IA)
{
this.IA = IA;
}