public static List <string> GetFormatsSuff()
{
List <string> suf;
loci.formats.ImageReader reader = new loci.formats.ImageReader();
suf = reader.getSuffixes().ToList();
reader = null;
for (int i = 0; i < suf.Count; i++)
{
suf[i] = "." + suf[i];
}
//Addapt
suf.Remove(".tif");
suf.Remove(".png");
suf.Remove(".jpg");
suf.Remove(".bmp");
suf.Remove(".txt");
suf.Remove(".xml");
suf.Remove(".csv");
return(suf);
}
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 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);
}
