BioImager.ImageJ Class Reference

Classes
class	Macro
class	RoiDecoder
class	RoiEncoder

Static Public Member Functions
static void	RunMacro (string file, string param)
static void	RunString (string con, string param, bool headless)
static void	RunOnImage (string con, bool headless, bool onTab, bool bioformats, bool newTab)
static bool	Initialize ()
static bool	SetImageJPath ()

Static Public Attributes
static List< Macro.Command >	Macros = new List<Macro.Command>()
static List< Process >	processes = new List<Process>()
static string	ImageJPath = Properties.Settings.Default.ImageJPath

Properties
static bool	Initialized [get]

Detailed Description

Definition at line 17 of file ImageJ.cs.

Member Function Documentation

Initialize()

static bool BioImager.ImageJ.Initialize ( )

static

This function is used to initialize the path of the ImageJ.exe file

Parameters

path	The path to the ImageJ executable.

Definition at line 247 of file ImageJ.cs.

        {
            if (!SetImageJPath())
                return false;
            Macro.Initialize();
            string[] ds = Directory.GetFiles(Path.GetDirectoryName(ImageJPath) + "/macros");
            foreach (string s in ds)
            {
                if (s.EndsWith(".ijm") || s.EndsWith(".txt"))
                    Macros.Add(new Macro.Command(Path.GetFileName(s), "", ""));
            }
            return true;
        }

References BioImager.ImageJ.SetImageJPath().

Referenced by BioImager.App.Initialize(), BioImager.ImageJ.RunMacro(), BioImager.ImageJ.RunOnImage(), and BioImager.ImageJ.RunString().

RunMacro()

static void BioImager.ImageJ.RunMacro ( string  file, string  param  )

static

It runs a macro in ImageJ

Parameters

file	the path to the macro file
param

Returns

The macro is being returned.

Definition at line 115 of file ImageJ.cs.

        {
            if(!Initialized)
            {
                Initialize();
            }
            file.Replace("/", "\\");
            Process pr = new Process();
            pr.StartInfo.FileName = ImageJPath;
            pr.StartInfo.Arguments = "-macro " + file + " " + param;
 
            pr.Start();
            processes.Add(pr);
            Recorder.AddLine("ImageJ.RunMacro(" + file + "," + '"' + param + '"' + ");");
        }

References BioImager.ImageJ.Initialize().

Referenced by BioImager.Imager.PerformFunction().

RunOnImage()

static void BioImager.ImageJ.RunOnImage ( string  con, bool  headless, bool  onTab, bool  bioformats, bool  newTab  )

static

It runs a macro on the selected image, saves the result as a new image, and then opens the new image in a new tab

Parameters

con	The ImageJ macro to run.
headless	Whether to run ImageJ in headless mode.
onTab	Whether to run the macro on current tab of images.
bioformats	If the image is a bioformats image, it will use the bioformats importer to open the image.
newTab	Whether or not the result should open in a new tab.

Returns

The return value is the result of the last statement in the script.

Definition at line 189 of file ImageJ.cs.

        {
            if (!Initialized)
            {
                Initialize();
            }
            string filename = "";
            string dir = Path.GetDirectoryName(ImageView.SelectedImage.file);
 
            if (ImageView.SelectedImage.ID.EndsWith(".ome.tif"))
            {
                filename = Path.GetFileNameWithoutExtension(ImageView.SelectedImage.ID);
                filename = filename.Remove(filename.Length - 4, 4);
            }
            else
                filename = Path.GetFileNameWithoutExtension(ImageView.SelectedImage.ID);
            string file = dir + "\\" + filename + "-temp" + ".ome.tif";
            file = file.Replace("\\", "/");
            string st =
            "run(\"Bio-Formats Importer\", \"open=\" + getArgument + \" autoscale color_mode=Default open_all_series display_rois rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT\"); " + con +
            "run(\"Bio-Formats Exporter\", \"save=" + file + " export compression=Uncompressed\"); " +
            "dir = getDir(\"startup\"); " +
            "File.saveString(\"done\", dir + \"/done.txt\");";
            if(bioformats)
                st =
                "open(getArgument); " + con +
                "run(\"Bio-Formats Exporter\", \"save=" + file + " export compression=Uncompressed\"); " +
                "dir = getDir(\"startup\"); " +
                "File.saveString(\"done\", dir + \"/done.txt\");";
            //We save the image as a temp image as otherwise imagej won't export due to file access error.
            RunString(st, ImageView.SelectedImage.file, headless);
 
            if (!File.Exists(file))
                return;
 
            string ffile = dir + "/" + filename + ".ome.tif";
            File.Delete(ffile);
            File.Copy(file, ffile);
            File.Delete(file);
            if (ImageView.SelectedImage.Filename != filename + ".ome.tif" || ImageView.SelectedImage.Filename != filename + ".tif")
            {
                if (ImageView.SelectedImage.filename.EndsWith(".tif"))
                    BioImage.OpenFile(ffile, newTab);
                else
                    BioImage.OpenFile(ffile, true);
            }
            else
            {
                App.viewer.Images[App.viewer.SelectedIndex] = BioImage.OpenFile(ffile, 0, false, false);
            }
            App.viewer.UpdateImage();
            App.viewer.UpdateView();
            Recorder.AddLine("RunOnImage(\"" + con + "\"," + headless + "," + onTab + "," + newTab + ");");
        }

References BioImager.ImageJ.Initialize(), BioImager.BioImage.OpenFile(), BioImager.ImageJ.RunString(), BioImager.ImageView.SelectedIndex, BioImager.ImageView.UpdateImage(), and BioImager.ImageView.UpdateView().

Referenced by BioImager.Function.PerformFunction().

RunString()

static void BioImager.ImageJ.RunString ( string  con, string  param, bool  headless  )

static

It runs a macro in ImageJ

Parameters

con	The macro code
param	The parameters to pass to the macro.
headless	whether or not to run ImageJ in headless mode

Returns

The macro is returning a string.

Definition at line 137 of file ImageJ.cs.

        {
            if (!Initialized)
            {
                Initialize();
            }
            Process pr = new Process();
            pr.StartInfo.FileName = ImageJPath;
            pr.StartInfo.CreateNoWindow = true;
            string te = rng.Next(0, 9999999).ToString();
            string p = Environment.CurrentDirectory + "\\" + te + ".txt";
            p.Replace("/", "\\");
            File.WriteAllText(p,con);
            if(headless)
                pr.StartInfo.Arguments = "--headless -macro " + p + " " + param;
            else
                pr.StartInfo.Arguments = "-macro " + p + " " + param;
            pr.Start();
            File.Delete(Path.GetDirectoryName(ImageJPath) + "/done.txt");
            processes.Add(pr);
            do
            {
                if (File.Exists(Path.GetDirectoryName(ImageJPath) + "/done.txt"))
                {
                    do
                    {
                        try
                        {
                            File.Delete(Path.GetDirectoryName(ImageJPath) + "/done.txt");
                        }
                        catch (Exception)
                        {
                        
                        }
                    } while (File.Exists(Path.GetDirectoryName(ImageJPath) + "/done.txt"));
                    pr.Kill();
                    break;
                }
            } while (!pr.HasExited);
            File.Delete(p);
        }

References BioImager.ImageJ.Initialize().

Referenced by BioImager.ImageJ.RunOnImage().

SetImageJPath()

static bool BioImager.ImageJ.SetImageJPath ( )

static

If the ImageJ path is not set, prompt the user to set it

Returns

The return value is a boolean.

Definition at line 263 of file ImageJ.cs.

        {
            if (Properties.Settings.Default.ImageJPath == "")
            {
                MessageBox.Show("ImageJ path not set. Set the ImageJ executable location.");
                OpenFileDialog file = new OpenFileDialog();
                file.Title = "Set the ImageJ executable location.";
                if (file.ShowDialog() != DialogResult.OK)
                    return false;
                Properties.Settings.Default.ImageJPath = file.FileName;
                Properties.Settings.Default.Save();
                ImageJPath = file.FileName;
                init = true;
                file.Dispose();
                return true;
            }
            else
                return true;
        }

Referenced by BioImager.ImageJ.Initialize().

Member Data Documentation

ImageJPath

string BioImager.ImageJ.ImageJPath = Properties.Settings.Default.ImageJPath

static

Definition at line 105 of file ImageJ.cs.

Macros

List<Macro.Command> BioImager.ImageJ.Macros = new List<Macro.Command>()

static

Definition at line 103 of file ImageJ.cs.

processes

List<Process> BioImager.ImageJ.processes = new List<Process>()

static

Definition at line 104 of file ImageJ.cs.

Property Documentation

Initialized

bool BioImager.ImageJ.Initialized

staticget

Definition at line 108 of file ImageJ.cs.

{ get { return init; } private set { } }

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The documentation for this class was generated from the following file:

• F:/repos/BioImager/BioImager/Source/ImageJ.cs