private void OpenFile(object sender, EventArgs e)
{
OpenFileDialog ofd = new OpenFileDialog();
string formatStr = "TIF files (*.tif)|*.tif|All files (*.*)|*.*";
/*
* foreach (string formatMiniStr in Interface.TabPages.myFileDecoder.Formats)
* {
* formatStr += "|" + formatMiniStr.Substring(1, formatMiniStr.Length - 1) +
* " files (*" + formatMiniStr + ")|*" + formatMiniStr;
* }*/
ofd.Filter = formatStr;
ofd.FilterIndex = 1;
ofd.RestoreDirectory = true;
if (ofd.ShowDialog() == DialogResult.OK)
{
TreeNode node = Interface.FileBrowser.CheckForFile(OSStringConverter.GetWinString(ofd.FileName));
if (node != null)
{
Interface.FileBrowser.Openlabel.Tag = node;
}
Interface.FileBrowser.Openlabel.Text = "'" + OSStringConverter.GetWinString(ofd.FileName) + "'";
Interface.FileBrowser.Openlabel.Text = "";
}
}
private static bool isLibTifCompatible(string dir)
{
if (!dir.EndsWith(".tif"))
{
return(false);
}
using (Tiff tif = Tiff.Open(OSStringConverter.StringToDir(dir), "r"))
{
if (tif == null)
{
tif.Close();
return(false);
}
try
{
tif.SetDirectory((short)(tif.NumberOfDirectories() - 1));
}
catch
{
tif.Close();
return(false);
}
int bitsPerPixel = tif.GetField(TiffTag.BITSPERSAMPLE)[0].ToInt();
tif.Close();
}
return(true);
}
private static string getLibTifFileDescription(string dir)
{
string des = "";
using (Tiff tif = Tiff.Open(OSStringConverter.StringToDir(dir), "r"))
{
if (tif == null)
{
return("");
}
tif.SetDirectory(0);
TiffTag tag = (TiffTag)270;
FieldValue[] value = tif.GetField(tag);
if (value != null)
{
for (int i = 0; i < value.Length; i++)
{
des += Encoding.UTF8.GetString(value[i].ToByteArray());
}
}
tif.Close();
}
return(des);
}
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(OSStringConverter.StringToDir(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);
}
private void Form_DragDropFiles(object sender, DragEventArgs e)
{
string[] dirList = e.Data.GetData(DataFormats.FileDrop) as string[];
foreach (string dir in dirList)
{
TreeNode node = Interface.FileBrowser.CheckForFile(OSStringConverter.GetWinString(dir));
if (node != null)
{
Interface.FileBrowser.Openlabel.Tag = node;
}
Interface.FileBrowser.Openlabel.Text = "'" + OSStringConverter.GetWinString(dir) + "'";
Interface.FileBrowser.Openlabel.Text = "";
}
}
private void PlugIns_TakeNames()
{
DeveloperToolStripMenuItem.DropDownItems.Clear();
ToolStripMenuItem InstallPlugInTS = new ToolStripMenuItem();
InstallPlugInTS.Text = "Install PlugIn";
InstallPlugInTS.Click += InstallPlugIn_Click;
DeveloperToolStripMenuItem.DropDownItems.Add(InstallPlugInTS);
ToolStripMenuItem UnInstallPlugInTS = new ToolStripMenuItem();
UnInstallPlugInTS.Text = "Uninstall PlugIn";
UnInstallPlugInTS.Click += UnInstallPlugIn_Click;
DeveloperToolStripMenuItem.DropDownItems.Add(UnInstallPlugInTS);
DeveloperToolStripMenuItem.DropDownItems.Add(new ToolStripSeparator());
// AddResultsExtractor();
// string path = Application.StartupPath + "\\PlugIns";
string path = OSStringConverter.StringToDir(
Environment.GetFolderPath(Environment.SpecialFolder.ApplicationData) + "\\CellToolPlugIns");
if (!Directory.Exists(path))
{
Directory.CreateDirectory(path);
}
DirectoryInfo directoryInfo = new DirectoryInfo(path);
foreach (var file in directoryInfo.GetFiles())
{
if (file.Name.EndsWith(".CTPlugIn.dll") &&
!file.Name.EndsWith("Results_Extractor.CTPlugIn.dll"))
{
string namePlugIn = file.Name.Replace(".CTPlugIn.dll", "").Replace("_", " ");
string dirPlugIn = file.FullName;
ToolStripMenuItem plugInTS = new ToolStripMenuItem();
plugInTS.Text = namePlugIn;
plugInTS.Tag = dirPlugIn;
plugInTS.Click += PlugInToolStripMenuItem_Click;
DeveloperToolStripMenuItem.DropDownItems.Add(plugInTS);
}
}
}
public void InstallPlugIn(string path)
{
path = OSStringConverter.GetWinString(path);
//background worker
var bgw = new BackgroundWorker();
bgw.WorkerReportsProgress = true;
//Add event for projection here
bgw.DoWork += new DoWorkEventHandler(delegate(Object o, DoWorkEventArgs a)
{
string newPath = OSStringConverter.StringToDir(
Environment.GetFolderPath(Environment.SpecialFolder.ApplicationData) + "\\CellToolPlugIns\\" +
path.Substring(path.LastIndexOf("\\") + 1, path.Length - path.LastIndexOf("\\") - 1));
if (File.Exists(newPath))
{
((BackgroundWorker)o).ReportProgress(1);
}
else
{
File.Copy(path, newPath, false);
((BackgroundWorker)o).ReportProgress(0);
}
});
bgw.ProgressChanged += new ProgressChangedEventHandler(delegate(Object o, ProgressChangedEventArgs a)
{
if (a.ProgressPercentage == 0)
{
PlugIns_TakeNames();
MessageBox.Show("Plugin installed!");
}
else if (a.ProgressPercentage == 1)
{
MessageBox.Show("Plugin already installed!"
);
}
IA.FileBrowser.StatusLabel.Text = "Ready";
});
//Start background worker
IA.FileBrowser.StatusLabel.Text = "Installing PlugIn...";
//start bgw
bgw.RunWorkerAsync();
}
private void Form_StartWithFile()
{
String[] dirList = Environment.GetCommandLineArgs();
if (dirList.Length > 0)
{
foreach (string dir in dirList)
{
if (dir.Length > 5)
{
if (dir.Substring(dir.Length - 4, 4) != ".exe")
{
TreeNode node = Interface.FileBrowser.CheckForFile(OSStringConverter.GetWinString(dir));
if (node != null)
{
Interface.FileBrowser.Openlabel.Tag = node;
}
Interface.FileBrowser.Openlabel.Text = "'" + OSStringConverter.GetWinString(dir) + "'";
Interface.FileBrowser.Openlabel.Text = "";
}
}
}
}
}
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 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(OSStringConverter.StringToDir(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(OSStringConverter.StringToDir(
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 void UnInstallPlugIn_Click(object sender, EventArgs e)
{
Form msgForm = new Form();
msgForm.Height = 600;
msgForm.Width = 600;
msgForm.Icon = Properties.Resources.CT_done;
msgForm.Text = "Uninstall PlugIns";
TreeView rtb = new TreeView();
rtb.CheckBoxes = true;
rtb.ShowLines = false;
rtb.Dock = DockStyle.Fill;
//Fill the box with names
string path = OSStringConverter.StringToDir(
Environment.GetFolderPath(Environment.SpecialFolder.ApplicationData) + "\\CellToolPlugIns");
bool unisntalled = false;
if (!Directory.Exists(path))
{
Directory.CreateDirectory(path);
}
DirectoryInfo directoryInfo = new DirectoryInfo(path);
foreach (var file in directoryInfo.GetFiles())
{
if (file.Name.EndsWith(".CTPlugIn.dll") &&
!file.Name.EndsWith("Results_Extractor.CTPlugIn.dll"))
{
string namePlugIn = file.Name.Replace(".CTPlugIn.dll", "").Replace("_", " ");
string dirPlugIn = file.FullName;
TreeNode n = new TreeNode(namePlugIn);
n.Checked = false;
n.Tag = dirPlugIn;
rtb.Nodes.Add(n);
}
}
//end filling
msgForm.Controls.Add(rtb);
Panel okBox = new Panel();
okBox.Height = 40;
okBox.Dock = DockStyle.Bottom;
msgForm.Controls.Add(okBox);
Button okBtn = new Button();
okBtn.Text = "Uninstall";
okBtn.BackColor = System.Drawing.SystemColors.ButtonFace;
okBtn.ForeColor = System.Drawing.Color.Black;
okBtn.Location = new System.Drawing.Point(20, 10);
okBtn.Anchor = AnchorStyles.Top | AnchorStyles.Left;
okBox.Controls.Add(okBtn);
Button cancelBtn = new Button();
cancelBtn.Text = "Cancel";
cancelBtn.BackColor = System.Drawing.SystemColors.ButtonFace;
cancelBtn.Location = new System.Drawing.Point(msgForm.Width - cancelBtn.Width - 40, 10);
cancelBtn.ForeColor = System.Drawing.Color.Black;
cancelBtn.Anchor = AnchorStyles.Top | AnchorStyles.Right;
okBox.Controls.Add(cancelBtn);
okBtn.Click += new EventHandler(delegate(object o, EventArgs a)
{
foreach (TreeNode n in rtb.Nodes)
{
if (n.Checked && File.Exists((string)n.Tag))
{
try
{
File.Delete((string)n.Tag);
unisntalled = true;
}
catch
{
MessageBox.Show(
"To uninstall the PlugIn, restart the program and try again!");
}
}
}
msgForm.Close();
});
cancelBtn.Click += new EventHandler(delegate(object o, EventArgs a)
{
msgForm.Close();
});
// Linux change
IA.FileBrowser.StatusLabel.Text = "Dialog open";
msgForm.ShowDialog();
IA.FileBrowser.StatusLabel.Text = "Ready";
if (unisntalled)
{
PlugIns_TakeNames();
MessageBox.Show("Selected plugins are uninstalled.");
}
msgForm.Dispose();
}