diff --git a/BioGTK.csproj b/BioGTK.csproj
index 22afce8..3bdf603 100644
--- a/BioGTK.csproj
+++ b/BioGTK.csproj
@@ -3,25 +3,25 @@
net8.0
Library
osx-x64;linux-x64;win-x64;win-arm64;linux-arm64;osx-arm64;
- 5.6.1
- 5.6.1
+ 5.7.0
+ 5.7.0
True
BioGTK
BioGTK
https://github.com/BiologyTools/BioGTK
banner.jpg
README.md
- 5.6.1
+ 5.7.0
https://github.com/BiologyTools/BioGTK
Biology; GTK; ImageJ; Bio-Formats; Image-Stacks; Microscopy; Whole-Slide-Image; Segment-Anything; SAM; QuPath;
GPL-3.0-only
True
A .NET application & library for editing & annotating various microscopy image formats. Supports all bioformats supported images. Integrates with ImageJ, running ImageJ filters & macro functions. Supports Windows, Linux and Mac.
- 5.6.1
+ 5.7.0
AnyCPU
True
AnyCPU
- CUDA support for Linux as well as MacOS related bug fixes.
+ CUDA support for Linux and Mac related bug fixes.
Erik Repo
@@ -49,13 +49,6 @@
7
-
-
-
-
-
-
-
PreserveNewest
@@ -411,16 +404,6 @@
True
true
-
- PreserveNewest
- True
- true
-
-
- PreserveNewest
- True
- true
-
PreserveNewest
@@ -472,14 +455,16 @@
BioGTK
BioGTK
com.BioGTK
- 5.6.1
+ 5.7.0
APPL
????
BioGTKApp
bio.icns
- 5.6.1
+ 5.7.0
NSApplication
true
enable
+ .ome.tif
+ OME-TIFF
diff --git a/Source/App.cs b/Source/App.cs
index f968cb2..bebe1f7 100644
--- a/Source/App.cs
+++ b/Source/App.cs
@@ -1,5 +1,6 @@
using Bio;
using Gtk;
+using javax.swing.filechooser;
using OpenSlideGTK;
using System;
using System.Collections.Generic;
@@ -87,15 +88,90 @@ private static void UpdateStitching()
SlideBase.UseVips = useVips;
}
- public static bool UseFiji = false;
+ public static bool ToConsole
+ {
+ get
+ {
+ return BioLib.Recorder.outputConsole;
+ }
+ set
+ {
+ BioLib.Recorder.outputConsole = value;
+ }
+ }
+ static bool useFiji = true;
+ public static bool UseFiji
+ {
+ get
+ {
+ if (OperatingSystem.IsMacOS())
+ {
+ return true;
+ }
+ else
+ {
+ if(Fiji.ImageJPath.Contains("Fiji"))
+ return true;
+ else
+ return false;
+ }
+ }
+ }
+ /// This function creates a file chooser dialog that allows the user to select the location of
+ /// the ImageJ executable
+ ///
+ /// @return A boolean value.
+ public static bool SetFijiOrImageJPath()
+ {
+ bool ifb;
+ string st = BioLib.Settings.GetSettings("ImageJPath");
+ if (st != "")
+ {
+ if (st.Contains("Fiji"))
+ {
+ BioLib.Fiji.ImageJPath = st;
+ }
+ else
+ BioLib.ImageJ.ImageJPath = st;
+ return true;
+ }
+ string title = "Select ImageJ Executable Location";
+ if (OperatingSystem.IsMacOS())
+ title = "Select ImageJ Executable Location (Fiji.app/Contents/MacOS/ImageJ-macosx)";
+ Gtk.FileChooserDialog filechooser =
+ new Gtk.FileChooserDialog(title, Scripting.window,
+ FileChooserAction.Open,
+ "Cancel", ResponseType.Cancel,
+ "Save", ResponseType.Accept);
+ filechooser.SetCurrentFolder(System.IO.Path.GetDirectoryName(Environment.ProcessPath));
+ if (filechooser.Run() != (int)ResponseType.Accept)
+ return false;
+ if(filechooser.Filename.Contains("Fiji"))
+ Fiji.ImageJPath = filechooser.Filename;
+ else
+ ImageJ.ImageJPath = filechooser.Filename;
+ BioLib.Settings.AddSettings("ImageJPath", filechooser.Filename);
+ filechooser.Destroy();
+ BioLib.Settings.Save();
+ return true;
+ }
/// Initialize() is a function that initializes the BioImage Suite Web
- public static void Initialize(bool requireImageJ = false)
+ public static void Initialize()
{
Console.WriteLine("Initializing components.");
- BioImage.Initialize();
+ SetFijiOrImageJPath();
+ if (Fiji.ImageJPath == "")
+ {
+ ImageJ.Initialize(ImageJ.ImageJPath);
+ BioImage.Initialize(ImageJ.ImageJPath);
+ }
+ else
+ {
+ Fiji.Initialize(Fiji.ImageJPath);
+ BioImage.Initialize(Fiji.ImageJPath);
+ }
Console.WriteLine("Loading settings.");
- Settings.Load();
- Fiji.Initialize(requireImageJ);
+ BioLib.Settings.Load();
updater = Updater.Create();
tools = Tools.Create();
filters = FiltersView.Create();
diff --git a/Source/BioConsole.cs b/Source/BioConsole.cs
index 356baf6..5b36fd7 100644
--- a/Source/BioConsole.cs
+++ b/Source/BioConsole.cs
@@ -234,7 +234,7 @@ private void ImagejBut_Clicked(object sender, EventArgs e)
{
if (ImageView.SelectedImage == null)
return;
- Fiji.RunOnImage(textBox.Buffer.Text, headless, onTab, useBioformats, resultsBox.Active);
+ Fiji.RunOnImage(ImageView.SelectedImage,textBox.Buffer.Text, headless, onTab, useBioformats, resultsBox.Active);
consoleBox.Buffer.Text += textBox.Buffer.Text + Environment.NewLine;
textBox.Buffer.Text = "";
}
diff --git a/Source/Fiji.cs b/Source/Fiji.cs
deleted file mode 100644
index 3d95fc7..0000000
--- a/Source/Fiji.cs
+++ /dev/null
@@ -1,1796 +0,0 @@
-using System;
-using System.Collections.Generic;
-using System.Linq;
-using System.Text;
-using System.Threading.Tasks;
-using System.Diagnostics;
-using System.IO;
-using CSScripting;
-using Gtk;
-using AForge;
-using BioGTK;
-using System.Runtime.InteropServices;
-using BioLib;
-using ij;
-using RectangleD = AForge.RectangleD;
-
-namespace BioGTK
-{
- public static class Fiji
- {
- public static class Macro
- {
- public class Command
- {
- public string Name { get; set; }
- public string Arguments { get; set; }
- public string Description { get; set; }
- public Command(string name, string args, string description)
- {
- Name = name;
- Arguments = args;
- Description = description;
- }
- public override string ToString()
- {
- return Name.ToString();
- }
- }
- public class Function
- {
- public string Name { get; set; }
- public string Arguments { get; set; }
- public string Description { get; set; }
- public Function(string name, string args, string description)
- {
- Name = name;
- Arguments = args;
- Description = description;
- }
- public override string ToString()
- {
- return Name.ToString();
- }
- }
- public static Dictionary Commands = new Dictionary();
- public static Dictionary> Functions = new Dictionary>();
- internal static void Initialize()
- {
- string[] sts = File.ReadAllLines(System.IO.Path.GetDirectoryName(Environment.ProcessPath) + "/macro-functions.txt");
- foreach (string s in sts)
- {
- string com = "";
- string args = "";
- string doc = "";
- bool indoc = false, inargs = false;
- if (!s.StartsWith('#'))
- {
- for (int i = 0; i < s.Length; i++)
- {
- if (!inargs)
- {
- if (s[i] != '(')
- com += s[i];
- else
- inargs = true;
- if (s[i] == ' ')
- {
- inargs = true;
- indoc = true;
- }
- }
- else
- if (!indoc)
- if (s[i] != ')')
- args += s[i];
- else
- indoc = true;
- else
- doc += s[i];
- }
- if (!Functions.ContainsKey(com))
- Functions.Add(com, new List() { new Function(com,args, doc) });
- else
- Functions[com].Add(new Function(com, args, doc));
- }
- }
- string[] cs = File.ReadAllLines(System.IO.Path.GetDirectoryName(Environment.ProcessPath) + "/macro-commands.csv");
- foreach (string s in cs)
- {
- string[] v = s.Split(',');
- Commands.Add(v[0], new Command(v[0], v[1], ""));
- }
- }
- }
- static bool init = false;
- public static bool Initialized { get { return init; } private set { init = true; } }
- public static string ImageJPath;
- public static string ImageJMacroPath
- {
- get
- {
- if(System.Runtime.InteropServices.RuntimeInformation.IsOSPlatform(OSPlatform.OSX))
- {
- string p = System.IO.Path.GetDirectoryName(ImageJPath);
- p = p.Remove(p.IndexOf("Fiji.app"), p.Length - p.IndexOf("Fiji.app"));
- return p + "/Fiji.app/macros";
- }
- else
- return System.IO.Path.GetDirectoryName(ImageJPath) + "/macros/";
- }
- }
- public static List processes = new List();
- public static List Macros = new List();
- private static Random rng = new Random();
- public static void RunImageJ(string file, string param)
- {
- Console.WriteLine("RunImageJ(" + file + "," + param);
- ImagePlus ip = ImageJ.GetImagePlus(ImageView.SelectedImage);
- Console.WriteLine("ImageJ.GetImagePlus(" + ImageView.SelectedImage.ToString() + ")");
- WindowManager.setTempCurrentImage(ip);
- Console.WriteLine("WindowManager.setTempCurrentImage(" +ip.ToString() + ")");
- IJ.runMacroFile(file, param);
- ImageView.SelectedImage = ImageJ.GetBioImage(ip, ImageView.SelectedImage.Volume, ImageView.SelectedImage.PhysicalSizeX, ImageView.SelectedImage.PhysicalSizeY, ImageView.SelectedImage.PhysicalSizeZ);
-
- }
- /// It runs a macro in ImageJ
- ///
- /// @param file the path to the macro file
- /// @param param The parameter to pass to the macro.
- ///
- /// @return The macro is being returned.
- public static void RunMacro(string file, string param, bool useFiji = false)
- {
- if (App.UseFiji || useFiji)
- {
- if (!Initialized)
- {
- if (!Initialize(true))
- return;
- }
- file.Replace("/", "\\");
- Process pr = new Process();
- pr.StartInfo.FileName = ImageJPath;
- pr.StartInfo.Arguments = "-macro " + file + " " + param;
- pr.Start();
- processes.Add(pr);
- }
- else
- {
- RunImageJ(file, param);
- }
- BioLib.Recorder.Record(BioLib.Recorder.GetCurrentMethodInfo(),false, file, param);
- }
- /// It runs a macro in ImageJ
- ///
- /// @param con The macro code
- /// @param param The parameters to pass to the macro.
- /// @param headless Whether or not to run ImageJ in headless mode.
- ///
- /// @return Nothing.
- public static void RunString(string con, string param, bool headless)
- {
- if (App.UseFiji)
- {
- if (!Initialized)
- {
- if (!Initialize(true))
- return;
- }
- Process pr = new Process();
- pr.StartInfo.FileName = ImageJPath;
- string te = rng.Next(0, 9999999).ToString();
- string p = Path.GetDirectoryName(Environment.ProcessPath) + "/" + te;
- if (OperatingSystem.IsMacOS())
- {
- Console.WriteLine(p);
- pr.StartInfo.UseShellExecute = true;
- }
- File.WriteAllText(p, con);
- if (headless)
- pr.StartInfo.Arguments = "--headless -macro " + p + " " + param;
- else
- pr.StartInfo.Arguments = "-macro " + p + " " + param;
- pr.Start();
- string donedir = Path.GetDirectoryName(Environment.ProcessPath);
- donedir = donedir.Replace("\\", "/");
- File.Delete(Path.GetDirectoryName(Environment.ProcessPath) + "/done.txt");
- processes.Add(pr);
- do
- {
- if (File.Exists(donedir + "/done.txt"))
- {
- do
- {
- try
- {
- File.Delete(donedir + "/done.txt");
- }
- catch (Exception)
- {
-
- }
- } while (File.Exists(donedir + "/done.txt"));
- pr.Kill();
- break;
- }
- } while (!pr.HasExited);
- File.Delete(p);
- }
- else
- {
- ImagePlus ip = ImageJ.GetImagePlus(ImageView.SelectedImage);
- WindowManager.setTempCurrentImage(ip);
- IJ.runMacro(con, param);
- ImageView.SelectedImage = ImageJ.GetBioImage(ip, ImageView.SelectedImage.Volume,ImageView.SelectedImage.PhysicalSizeX, ImageView.SelectedImage.PhysicalSizeY, ImageView.SelectedImage.PhysicalSizeZ);
- }
- }
- /// It runs a macro on the current image, saves the result as a new image, and then opens the
- /// new image in a new tab
- ///
- /// @param con The ImageJ macro to run on the image.
- /// @param headless Whether to run ImageJ in headless mode.
- /// @param onTab If true, the imacro will be run on tab. If false, the macro will be run on selected image.
- /// @param bioformats If true, the image is opened using the bioformats plugin. If false, the
- /// image is opened using the default imagej open command.
- ///
- /// @return The image is being returned as a new tab.
- public static void RunOnImage(string con, int index, bool headless, bool onTab, bool bioformats, bool resultInNewTab)
- {
- if (App.UseFiji)
- {
- if (!Initialized)
- {
- if (!Initialize(true))
- return;
- }
- string filename = "";
- string dir = Path.GetDirectoryName(ImageView.SelectedImage.file);
- dir = dir.Replace("\\", "/");
- 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";
- if (!bioformats)
- file = dir + "/" + filename + ".tif";
- string donepath = Path.GetDirectoryName(Environment.ProcessPath);
- donepath = donepath.Replace("\\", "/");
- string op = dir + "/" + ImageView.SelectedImage.ID.Replace("\\", "/");
- if (!File.Exists(op))
- {
- BioImage.SaveOME(ImageView.SelectedImage, op);
- }
- string st =
- "run(\"Bio-Formats Importer\", \"open=" + op + " 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 = \"" + donepath + "\"" +
- "File.saveString(\"done\", dir + \"/done.txt\");";
- if (!bioformats)
- st =
- "open(getArgument); " + con +
- "saveAs(\"Tiff\",\"" + file + "\"); " +
- "dir = \"" + donepath + "\"" +
- "File.saveString(\"done\", dir + \"/done.txt\");";
- if (File.Exists(file) && bioformats)
- File.Delete(file);
- RunString(st, dir + "/" + ImageView.SelectedImage.ID, headless);
- if (!File.Exists(file))
- return;
- //If not in images we add it to a new tab.
- if (Images.GetImage(file) == null)
- {
- BioImage bm = BioImage.OpenFile(file, index, false, false);
- bm.ID = Path.GetFileName(file).Replace("-temp", "");
- bm.Filename = bm.ID;
- bm.file = file;
- Images.AddImage(bm);
- }
- else
- {
- BioImage b = BioImage.OpenFile(file, index, onTab, false);
- b.ID = ImageView.SelectedImage.ID;
- b.Filename = ImageView.SelectedImage.Filename;
- b.file = dir + "/" + ImageView.SelectedImage.ID;
- Images.UpdateImage(b);
- App.viewer.Images[App.viewer.SelectedIndex] = b;
- }
- //If using bioformats we delete the temp file.
- if (bioformats)
- File.Delete(file);
- // update image on main UI thread
- if (App.viewer != null)
- {
- Application.Invoke(delegate
- {
- App.viewer.UpdateImage();
- App.viewer.UpdateView();
- });
- }
- BioLib.Recorder.Record(BioLib.Recorder.GetCurrentMethodInfo(), false,con, index, headless, onTab, bioformats, resultInNewTab);
- }
- else
- {
- cons = con;
- indexs = index;
- headlesss = headless;
- onTabs = onTab;
- bioformatss = bioformats;
- resultInNewTabs = resultInNewTab;
- Thread th = new Thread(RunImageJ);
- th.Start();
- }
- }
-
- static string cons;
- static int indexs;
- static bool headlesss;
- static bool onTabs;
- static bool bioformatss;
- static bool resultInNewTabs;
- private static void RunImageJ()
- {
- ImagePlus ip = ImageJ.GetImagePlus(ImageView.SelectedImage);
- WindowManager.setTempCurrentImage(ip);
- try
- {
- IJ.runMacro(cons);
- ImageView.SelectedImage = ImageJ.GetBioImage(ip, ImageView.SelectedImage.Volume, ImageView.SelectedImage.PhysicalSizeX, ImageView.SelectedImage.PhysicalSizeY, ImageView.SelectedImage.PhysicalSizeZ);
- }
- catch (Exception e)
- {
- Console.WriteLine(e.Message.ToString());
- }
- }
- public static void RunOnImage(string s)
- {
- RunOnImage(s, BioConsole.headless, BioConsole.onTab, BioConsole.useBioformats, BioConsole.resultInNewTab);
- }
- public static void RunOnImage(string con, bool headless, bool onTab, bool bioformats, bool resultInNewTab)
- {
- RunOnImage(con,0,headless,onTab,bioformats,resultInNewTab);
- }
- /// This function is used to initialize the path of the ImageJ.exe file
- ///
- /// @param path The path to the ImageJ executable.
- public static bool Initialize(bool imagej)
- {
- if (!imagej)
- return false;
- if (!SetImageJPath())
- return false;
- Macro.Initialize();
- string[] ds = Directory.GetFiles(ImageJMacroPath);
- foreach (string s in ds)
- {
- if(s.EndsWith(".ijm") || s.EndsWith(".txt"))
- Macros.Add(new Macro.Command(Path.GetFileName(s), "", ""));
- }
- return true;
- }
-
- /// This function creates a file chooser dialog that allows the user to select the location of
- /// the ImageJ executable
- ///
- /// @return A boolean value.
- public static bool SetImageJPath()
- {
- string st = Settings.GetSettings("ImageJPath");
- if(st!="")
- {
- Initialized = true;
- ImageJPath = Settings.GetSettings("ImageJPath");
- return true;
- }
- string title = "Select ImageJ Executable Location";
- if (OperatingSystem.IsMacOS())
- title = "Select ImageJ Executable Location (Fiji.app/Contents/MacOS/ImageJ-macosx)";
- Gtk.FileChooserDialog filechooser =
- new Gtk.FileChooserDialog(title, Scripting.window,
- FileChooserAction.Open,
- "Cancel", ResponseType.Cancel,
- "Save", ResponseType.Accept);
- filechooser.SetCurrentFolder(System.IO.Path.GetDirectoryName(Environment.ProcessPath));
- if (filechooser.Run() != (int)ResponseType.Accept)
- return false;
- Fiji.ImageJPath = filechooser.Filename;
- Settings.AddSettings("ImageJPath", filechooser.Filename);
- filechooser.Destroy();
- Settings.Save();
- Initialized = true;
- return true;
- }
-
- public class RoiDecoder
- {
- #region Params
- // offsets
- public static int VERSION_OFFSET = 4;
- public static int TYPE = 6;
- public static int TOP = 8;
- public static int LEFT = 10;
- public static int BOTTOM = 12;
- public static int RIGHT = 14;
- public static int N_COORDINATES = 16;
- public static int X1 = 18;
- public static int Y1 = 22;
- public static int X2 = 26;
- public static int Y2 = 30;
- public static int XD = 18;
- public static int YD = 22;
- public static int WIDTHD = 26;
- public static int HEIGHTD = 30;
- public static int SIZE = 18;
- public static int STROKE_WIDTH = 34;
- public static int SHAPE_ROI_SIZE = 36;
- public static int STROKE_COLOR = 40;
- public static int FILL_COLOR = 44;
- public static int SUBTYPE = 48;
- public static int OPTIONS = 50;
- public static int ARROW_STYLE = 52;
- public static int FLOAT_PARAM = 52; //ellipse ratio or rotated rect width
- public static int POINT_TYPE = 52;
- public static int ARROW_HEAD_SIZE = 53;
- public static int ROUNDED_RECT_ARC_SIZE = 54;
- public static int POSITION = 56;
- public static int HEADER2_OFFSET = 60;
- public static int COORDINATES = 64;
- // header2 offsets
- public static int C_POSITION = 4;
- public static int Z_POSITION = 8;
- public static int T_POSITION = 12;
- public static int NAME_OFFSET = 16;
- public static int NAME_LENGTH = 20;
- public static int OVERLAY_LABEL_COLOR = 24;
- public static int OVERLAY_FONT_SIZE = 28; //short
- public static int GROUP = 30; //byte
- public static int IMAGE_OPACITY = 31; //byte
- public static int IMAGE_SIZE = 32; //int
- public static int FLOAT_STROKE_WIDTH = 36; //float
- public static int ROI_PROPS_OFFSET = 40;
- public static int ROI_PROPS_LENGTH = 44;
- public static int COUNTERS_OFFSET = 48;
-
- // subtypes
- public static int TEXT = 1;
- public static int ARROW = 2;
- public static int ELLIPSE = 3;
- public static int IMAGE = 4;
- public static int ROTATED_RECT = 5;
-
- // options
- public static int SPLINE_FIT = 1;
- public static int DOUBLE_HEADED = 2;
- public static int OUTLINE = 4;
- public static int OVERLAY_LABELS = 8;
- public static int OVERLAY_NAMES = 16;
- public static int OVERLAY_BACKGROUNDS = 32;
- public static int OVERLAY_BOLD = 64;
- public static int SUB_PIXEL_RESOLUTION = 128;
- public static int DRAW_OFFSET = 256;
- public static int ZERO_TRANSPARENT = 512;
- public static int SHOW_LABELS = 1024;
- public static int SCALE_LABELS = 2048;
- public static int PROMPT_BEFORE_DELETING = 4096; //points
- public static int SCALE_STROKE_WIDTH = 8192;
-
- // types
- private int polygon = 0, rect = 1, oval = 2, line = 3, freeline = 4, polyline = 5, noRoi = 6,
- freehand = 7, traced = 8, angle = 9, point = 10;
-
- private byte[] data;
- private string path;
- private MemoryStream ins;
- private string name;
- private int size;
- #endregion
-
- /** Constructs an RoiDecoder using a file path. */
- public RoiDecoder(string path)
- {
- this.path = path;
- }
-
- /** Constructs an RoiDecoder using a byte array. */
- public RoiDecoder(byte[] bytes, string name)
- {
- ins = new MemoryStream(bytes);
- this.name = name;
- this.size = bytes.Length;
- }
-
- /** Opens the ROI at the specified path. Returns null if there is an error. */
- public static ROI open(string path)
- {
- ROI roi = null;
- RoiDecoder rd = new RoiDecoder(path);
- roi = rd.getRoi();
- return roi;
- }
-
- /** Returns the ROI. */
- public ROI getRoi()
- {
- ROI roi = new ROI();
- data = File.ReadAllBytes(path);
- size = data.Length;
- if (getByte(0) != 73 || getByte(1) != 111) //"Iout"
- throw new IOException("This is not an ImageJ ROI");
- int version = getShort(VERSION_OFFSET);
- int type = getByte(TYPE);
- int subtype = getShort(SUBTYPE);
- int top = getShort(TOP);
- int left = getShort(LEFT);
- int bottom = getShort(BOTTOM);
- int right = getShort(RIGHT);
- int width = right - left;
- int height = bottom - top;
- int n = getUnsignedShort(N_COORDINATES);
- if (n == 0)
- n = getInt(SIZE);
- int options = getShort(OPTIONS);
- int position = getInt(POSITION);
- int hdr2Offset = getInt(HEADER2_OFFSET);
- int channel = 0, slice = 0, frame = 0;
- int overlayLabelColor = 0;
- int overlayFontSize = 0;
- int group = 0;
- int imageOpacity = 0;
- int imageSize = 0;
- bool subPixelResolution = (options & SUB_PIXEL_RESOLUTION) != 0 && version >= 222;
- bool drawOffset = subPixelResolution && (options & DRAW_OFFSET) != 0;
- bool scaleStrokeWidth = true;
- if (version >= 228)
- scaleStrokeWidth = (options & SCALE_STROKE_WIDTH) != 0;
-
- bool subPixelRect = version >= 223 && subPixelResolution && (type == rect || type == oval);
- double xd = 0.0, yd = 0.0, widthd = 0.0, heightd = 0.0;
- if (subPixelRect) {
- xd = getFloat(XD);
- yd = getFloat(YD);
- widthd = getFloat(WIDTHD);
- heightd = getFloat(HEIGHTD);
- roi.subPixel = true;
- }
-
- if (hdr2Offset > 0 && hdr2Offset + IMAGE_SIZE + 4 <= size)
- {
- channel = getInt(hdr2Offset + C_POSITION);
- slice = getInt(hdr2Offset + Z_POSITION);
- frame = getInt(hdr2Offset + T_POSITION);
- overlayLabelColor = getInt(hdr2Offset + OVERLAY_LABEL_COLOR);
- overlayFontSize = getShort(hdr2Offset + OVERLAY_FONT_SIZE);
- imageOpacity = getByte(hdr2Offset + IMAGE_OPACITY);
- imageSize = getInt(hdr2Offset + IMAGE_SIZE);
- group = getByte(hdr2Offset + GROUP);
- }
-
- if (name != null && name.EndsWith(".roi"))
- name = name.Substring(0, name.Length - 4);
- bool isComposite = getInt(SHAPE_ROI_SIZE) > 0;
-
-
- /*
- if (isComposite)
- {
- roi = getShapeRoi();
- if (version >= 218)
- getStrokeWidthAndColor(roi, hdr2Offset, scaleStrokeWidth);
- roi.coord.Z = position;
- if (channel > 0 || slice > 0 || frame > 0)
- {
- roi.coord.C = channel; roi.coord.Z = slice; roi.coord.T = frame;
- }
- decodeOverlayOptions(roi, version, options, overlayLabelColor, overlayFontSize);
- if (version >= 224)
- {
- string props = getRoiProps();
- if (props != null)
- roi.properties = props;
- }
- if (version >= 228 && group > 0)
- roi.serie = group;
- return roi;
- }
- */
- switch (type)
- {
- case 1: //Rect
- if (subPixelRect)
- roi = ROI.CreateRectangle(new AForge.ZCT(slice-1, channel - 1, frame - 1), xd, yd, widthd, heightd);
- else
- roi = ROI.CreateRectangle(new AForge.ZCT(slice - 1, channel - 1, frame - 1), left, top, width, height);
- int arcSize = getShort(ROUNDED_RECT_ARC_SIZE);
- if (arcSize > 0)
- throw new NotSupportedException("Type rounded rectangle not supported.");
- break;
- case 2: //Ellipse
- if (subPixelRect)
- roi = ROI.CreateEllipse(new AForge.ZCT(slice - 1, channel - 1, frame - 1), xd, yd, widthd, heightd);
- else
- roi = ROI.CreateEllipse(new AForge.ZCT(slice - 1, channel - 1, frame - 1), left, top, width, height);
- break;
- case 3: //Line
- float x1 = getFloat(X1);
- float y1 = getFloat(Y1);
- float x2 = getFloat(X2);
- float y2 = getFloat(Y2);
-
- if (subtype == ARROW)
- {
- throw new NotSupportedException("Type arrow not supported.");
- /*
- roi = new Arrow(x1, y1, x2, y2);
- ((Arrow)roi).setDoubleHeaded((options & DOUBLE_HEADED) != 0);
- ((Arrow)roi).setOutline((options & OUTLINE) != 0);
- int style = getByte(ARROW_STYLE);
- if (style >= Arrow.FILLED && style <= Arrow.BAR)
- ((Arrow)roi).setStyle(style);
- int headSize = getByte(ARROW_HEAD_SIZE);
- if (headSize >= 0 && style <= 30)
- ((Arrow)roi).setHeadSize(headSize);
- */
- }
- else
- {
- roi = ROI.CreateLine(new AForge.ZCT(slice, channel, frame), new AForge.PointD(x1, y1), new AForge.PointD(x2, y2));
- //roi.setDrawOffset(drawOffset);
- }
-
- break;
- case 0:
- case 5:
- case 6:
- case 7:
- case 8:
- case 9:
- case 10:
- //IJ.log("type: "+type);
- //IJ.log("n: "+n);
- //ij.IJ.log("rect: "+left+","+top+" "+width+" "+height);
- if (n == 0 || n < 0) break;
- int[] x = new int[n];
- int[] y = new int[n];
- float[] xf = null;
- float[] yf = null;
- int base1 = COORDINATES;
- int base2 = base1 + 2 * n;
- int xtmp, ytmp;
- for (int i = 0; i < n; i++)
- {
- xtmp = getShort(base1 + i * 2);
- if (xtmp < 0) xtmp = 0;
- ytmp = getShort(base2 + i * 2);
- if (ytmp < 0) ytmp = 0;
- x[i] = left + xtmp;
- y[i] = top + ytmp;
- }
- if (subPixelResolution)
- {
- xf = new float[n];
- yf = new float[n];
- base1 = COORDINATES + 4 * n;
- base2 = base1 + 4 * n;
- for (int i = 0; i < n; i++)
- {
- xf[i] = getFloat(base1 + i * 4);
- yf[i] = getFloat(base2 + i * 4);
- }
- }
- if (type == point)
- {
- //TODO implement non subpizel ROI
- if (subPixelResolution)
- {
- roi.AddPoints(xf, yf);
- }
- else
- roi.AddPoints(x, y);
- if (version >= 226)
- {
- //((PointRoi)roi).setPointType(getByte(POINT_TYPE));
- roi.strokeWidth = getShort(STROKE_WIDTH);
- }
- //if ((options & SHOW_LABELS) != 0 && !ij.Prefs.noPointLabels)
- // ((PointRoi)roi).setShowLabels(true);
- //if ((options & PROMPT_BEFORE_DELETING) != 0)
- // ((PointRoi)roi).promptBeforeDeleting(true);
- roi.type = ROI.Type.Point;
- break;
- }
- if (type == polygon)
- roi.type = ROI.Type.Polygon;
- else if (type == freehand)
- {
- roi.type = ROI.Type.Freeform;
- if (subtype == ELLIPSE || subtype == ROTATED_RECT)
- {
- throw new NotSupportedException("ROI type not supported.");
- /*
- double ex1 = getFloat(X1);
- double ey1 = getFloat(Y1);
- double ex2 = getFloat(X2);
- double ey2 = getFloat(Y2);
- double param = getFloat(FLOAT_PARAM);
- if (subtype == ROTATED_RECT)
- roi = new RotatedRectRoi(ex1, ey1, ex2, ey2, param);
- else
- roi = new EllipseRoi(ex1, ey1, ex2, ey2, param);
- break;
- */
- }
- }
- else if (type == traced)
- roi.type = ROI.Type.Polyline;
- else if (type == polyline)
- roi.type = ROI.Type.Polyline;
- else if (type == freeline)
- roi.type = ROI.Type.Polyline;
- else if (type == angle)
- roi.type = ROI.Type.Point;
- else
- roi.type = ROI.Type.Freeform;
- if (subPixelResolution)
- {
- roi.AddPoints(xf, yf);
- //roi = new PolygonRoi(xf, yf, n, roiType);
- //roi.setDrawOffset(drawOffset);
- }
- else
- roi.AddPoints(x, y);
- break;
- default:
- throw new IOException("Unrecognized ROI type: " + type);
- }
- if (roi == null)
- return null;
- roi.roiName = getRoiName();
-
- // read stroke width, stroke color and fill color (1.43i or later)
- if (version >= 218)
- {
- getStrokeWidthAndColor(roi, hdr2Offset, scaleStrokeWidth);
- /*
- if (type == point)
- roi.setStrokeWidth(0);
- bool splineFit = (options & SPLINE_FIT) != 0;
- if (splineFit && roi instanceof PolygonRoi)
- ((PolygonRoi)roi).fitSpline();
- */
- }
-
- if (version >= 218 && subtype == TEXT)
- {
- getTextRoi(roi, version);
- roi.type = ROI.Type.Label;
- }
- /*
- if (version >= 221 && subtype == IMAGE)
- roi = getImageRoi(roi, imageOpacity, imageSize, options);
-
- if (version >= 224)
- {
- string props = getRoiProps();
- if (props != null)
- roi.setProperties(props);
- }
-
- if (version >= 227)
- {
- int[] counters = getPointCounters(n);
- if (counters != null && (roi instanceof PointRoi))
- ((PointRoi)roi).setCounters(counters);
- }
- */
- // set group (1.52t or later)
- if (version >= 228 && group > 0)
- roi.serie = group;
-
- roi.coord.Z = position;
- if (channel > 0 || slice > 0 || frame > 0)
- roi.coord = new AForge.ZCT(slice - 1, channel - 1, frame - 1); //-1 because our ROI coordinates are 0 based
- //decodeOverlayOptions(roi, version, options, overlayLabelColor, overlayFontSize);
-
- //We convert pixel to subpixel
- if (!roi.subPixel)
- {
- for (int i = 0; i < roi.PointsD.Count; i++)
- {
- AForge.PointD pd = ImageView.SelectedImage.ToStageSpace(roi.PointsD[i]);
- roi.PointsD[i] = pd;
- roi.UpdateBoundingBox();
- }
- }
- if (roi.type == ROI.Type.Polygon || roi.type == ROI.Type.Freeform)
- roi.closed = true;
- return roi;
- }
- /*
- void decodeOverlayOptions(ROI roi, int version, int options, int color, int fontSize)
- {
-
- Overlay proto = new Overlay();
- proto.drawLabels((options & OVERLAY_LABELS) != 0);
- proto.drawNames((options & OVERLAY_NAMES) != 0);
- proto.drawBackgrounds((options & OVERLAY_BACKGROUNDS) != 0);
- if (version >= 220 && color != 0)
- proto.setLabelColor(new Color(color));
- bool bold = (options & OVERLAY_BOLD) != 0;
- bool scalable = (options & SCALE_LABELS) != 0;
- if (fontSize > 0 || bold || scalable)
- {
- proto.setLabelFont(new Font("SansSerif", bold ? Font.BOLD : Font.PLAIN, fontSize), scalable);
- }
- roi.setPrototypeOverlay(proto);
-
- }
- */
- void getStrokeWidthAndColor(ROI roi, int hdr2Offset, bool scaleStrokeWidth)
- {
- double strokeWidth = getShort(STROKE_WIDTH);
- if (hdr2Offset > 0)
- {
- double strokeWidthD = getFloat(hdr2Offset + FLOAT_STROKE_WIDTH);
- if (strokeWidthD > 0.0)
- strokeWidth = strokeWidthD;
- }
- if (strokeWidth > 0.0)
- {
- roi.strokeWidth = strokeWidth;
- }
- int strokeColor = getInt(STROKE_COLOR);
- if (strokeColor != 0)
- {
- byte[] bts = BitConverter.GetBytes(strokeColor);
- AForge.Color c = AForge.Color.FromArgb(bts[0], bts[1], bts[2], bts[3]);
- roi.strokeColor = c;
- }
- int fillColor = getInt(FILL_COLOR);
- if (fillColor != 0)
- {
- byte[] bts = BitConverter.GetBytes(strokeColor);
- AForge.Color c = AForge.Color.FromArgb(bts[0], bts[1], bts[2], bts[3]);
- roi.fillColor = c;
- }
- }
- /*
- public ROI getShapeRoi()
- {
- int type = getByte(TYPE);
- if (type!=rect)
- throw new NotSupportedException("Invalid composite ROI type");
- int top = getShort(TOP);
- int left = getShort(LEFT);
- int bottom = getShort(BOTTOM);
- int right = getShort(RIGHT);
- int width = right - left;
- int height = bottom - top;
- int n = getInt(SHAPE_ROI_SIZE);
-
- ROI roi = new ROI();
- float[] shapeArray = new float[n];
- int bas = COORDINATES;
- for (int i = 0; i < n; i++)
- {
- shapeArray[i] = getFloat(bas);
- bas += 4;
- }
- roi = new ShapeRoi(shapeArray);
- roi.setName(getRoiName());
- return roi;
- }
- */
- void getTextRoi(ROI roi, int version)
- {
- AForge.Rectangle r = roi.BoundingBox.ToRectangleInt();
- int hdrSize = 64;
- int size = getInt(hdrSize);
- int styleAndJustification = getInt(hdrSize + 4);
- int style = styleAndJustification & 255;
- int justification = (styleAndJustification >> 8) & 3;
- bool drawStringMode = (styleAndJustification & 1024) != 0;
- int nameLength = getInt(hdrSize + 8);
- int textLength = getInt(hdrSize + 12);
- char[] name = new char[nameLength];
- char[] text = new char[textLength];
- for (int i = 0; i < nameLength; i++)
- name[i] = (char)getShort(hdrSize + 16 + i * 2);
- for (int i = 0; i < textLength; i++)
- text[i] = (char)getShort(hdrSize + 16 + nameLength * 2 + i * 2);
- double angle = version >= 225 ? getFloat(hdrSize + 16 + nameLength * 2 + textLength * 2) : 0f;
- //Font font = new Font(new string(name), style, size);
- roi.family = new string(name);
- roi.Text = new string(text);
- roi.slant = Cairo.FontSlant.Normal;
- roi.weight = Cairo.FontWeight.Normal;
- roi.fontSize = size;
- /*
- if (roi.subPixel)
- {
- RectangleD fb = roi.Rect;
- roi2 = new TextRoi(fb.getX(), fb.getY(), fb.getWidth(), fb.getHeight(), new string(text), font);
- }
- else
- roi2 = new TextRoi(r.x, r.y, r.width, r.height, new string(text), font);
-
- roi.strokeColor
- roi2.setFillColor(roi.getFillColor());
- roi2.setName(getRoiName());
- roi2.setJustification(justification);
- roi2.setDrawStringMode(drawStringMode);
- roi2.setAngle(angle);
- return roi2;
- */
- }
-
- string getRoiName()
- {
- string fileName = name;
- int hdr2Offset = getInt(HEADER2_OFFSET);
- if (hdr2Offset == 0)
- return fileName;
- int offset = getInt(hdr2Offset + NAME_OFFSET);
- int Length = getInt(hdr2Offset + NAME_LENGTH);
- if (offset == 0 || Length == 0)
- return fileName;
- if (offset + Length * 2 > size)
- return fileName;
- char[] namem = new char[Length];
- for (int i = 0; i < Length; i++)
- namem[i] = (char)getShort(offset + i * 2);
- return new string(namem);
- }
-
- string getRoiProps()
- {
- int hdr2Offset = getInt(HEADER2_OFFSET);
- if (hdr2Offset == 0)
- return null;
- int offset = getInt(hdr2Offset + ROI_PROPS_OFFSET);
- int Length = getInt(hdr2Offset + ROI_PROPS_LENGTH);
- if (offset == 0 || Length == 0)
- return null;
- if (offset + Length * 2 > size)
- return null;
- char[] props = new char[Length];
- for (int i = 0; i < Length; i++)
- props[i] = (char)getShort(offset + i * 2);
- return new string(props);
- }
-
- int[] getPointCounters(int n)
- {
- int hdr2Offset = getInt(HEADER2_OFFSET);
- if (hdr2Offset == 0)
- return null;
- int offset = getInt(hdr2Offset + COUNTERS_OFFSET);
- if (offset == 0)
- return null;
- if (offset + n * 4 > data.Length)
- return null;
- int[] counters = new int[n];
- for (int i = 0; i < n; i++)
- counters[i] = getInt(offset + i * 4);
- return counters;
- }
-
-
- int getByte(int bas)
- {
- return data[bas] & 255;
- }
-
- int getShort(int bas)
- {
- int b0 = data[bas] & 255;
- int b1 = data[bas + 1] & 255;
- int n = (short)((b0 << 8) + b1);
- if (n < -5000)
- n = (b0 << 8) + b1; // assume n>32767 and unsigned
- return n;
- }
-
- int getUnsignedShort(int bas)
- {
- int b0 = data[bas] & 255;
- int b1 = data[bas + 1] & 255;
- return (b0 << 8) + b1;
- }
-
- int getInt(int bas)
- {
- int b0 = data[bas] & 255;
- int b1 = data[bas + 1] & 255;
- int b2 = data[bas + 2] & 255;
- int b3 = data[bas + 3] & 255;
- return ((b0 << 24) + (b1 << 16) + (b2 << 8) + b3);
- }
-
- float getFloat(int bas)
- {
- return BitConverter.Int32BitsToSingle(getInt(bas));
- }
-
- /** Opens an ROI from a byte array. */
- public static ROI openFromByteArray(byte[] bytes)
- {
- ROI roi = null;
- if (bytes == null || bytes.Length == 0)
- return roi;
- try
- {
- RoiDecoder decoder = new RoiDecoder(bytes, null);
- roi = decoder.getRoi();
- }
- catch (IOException e)
- {
- return null;
- }
- return roi;
- }
-
- }
-
- /// The function `GetImageJType` takes in a `ROI` object and returns an integer representing the
- /// type of the ROI in ImageJ.
- ///
- /// @param ROI The ROI parameter is an object of type ROI, which represents a region of interest
- /// in an image. It has a property called "type" which indicates the type of the ROI.
- ///
- /// @return The method is returning an integer value that represents the ImageJ type of the
- /// given ROI.
- static int GetImageJType(ROI roi)
- {
- //private int polygon = 0, rect = 1, oval = 2, line = 3, freeline = 4, polyline = 5, noRoi = 6, freehand = 7,
- // traced = 8, angle = 9, point = 10;
- switch (roi.type)
- {
- case ROI.Type.Rectangle:
- return 1;
- case ROI.Type.Point:
- return 10;
- case ROI.Type.Line:
- return 3;
- case ROI.Type.Polygon:
- return 0;
- case ROI.Type.Polyline:
- return 5;
- case ROI.Type.Freeform:
- return 7;
- case ROI.Type.Ellipse:
- return 2;
- case ROI.Type.Label:
- default:
- return 0;
- }
- }
-
- /// The function "GetPointsXY" takes a ROI object and returns the X and Y coordinates of its
- /// points as arrays.
- ///
- /// @param ROI The ROI parameter is an object that represents a region of interest. It contains
- /// a collection of points (PointsD) that define the boundary of the region.
- /// @param xp An array of integers representing the x-coordinates of the points in the ROI.
- /// @param yp The `yp` parameter is an output parameter of type `int[]`. It is used to return
- /// the y-coordinates of the points in the `ROI` object.
- static void GetPointsXY(ROI roi, out int[] xp, out int[] yp)
- {
- int[] x = new int[roi.PointsD.Count];
- int[] y = new int[roi.PointsD.Count];
- for (int i = 0; i < roi.PointsD.Count; i++)
- {
- PointD pd = ImageView.SelectedImage.ToImageSpace(roi.PointsD[i]);
- x[i] = (int)pd.X;
- y[i] = (int)pd.Y;
- }
- xp = x;
- yp = y;
-
- }
-
- /// The function "GetXY" takes a region of interest (ROI) and returns the corresponding X and Y
- /// coordinates in image space.
- ///
- /// @param ROI The ROI parameter is of type ROI, which is likely a custom class representing a
- /// region of interest. It contains information about the position and size of the region.
- /// @param x An output parameter that will store the X coordinate of the ROI in image space.
- /// @param y The "y" parameter is an output parameter that will hold the y-coordinate of the ROI
- /// (Region of Interest) after the method is called.
- static void GetXY(ROI roi,out float x, out float y)
- {
- PointD pd = ImageView.SelectedImage.ToImageSpace(new PointD(roi.X,roi.Y));
- x = (float)pd.X;
- y = (float)pd.Y;
- }
- /// The function "GetWH" takes a ROI (region of interest) and returns the width and height of
- /// the ROI in terms of image size.
- ///
- /// @param ROI The ROI parameter is an object that represents a region of interest. It likely
- /// contains information such as the position (x, y) and size (width, height) of the region.
- /// @param w The width of the ROI (Region of Interest) in the selected image.
- /// @param h The "h" parameter is an output parameter of type float. It is used to store the
- /// height value calculated in the method.
- static void GetWH(ROI roi, out float w, out float h)
- {
- w = (float)ImageView.SelectedImage.ToImageSizeX(roi.W);
- h = (float)ImageView.SelectedImage.ToImageSizeY(roi.H);
- }
- /// The function rightMove takes an integer value and a position as input, and returns the value
- /// after performing a right shift operation by the specified position.
- ///
- /// @param value The value is an integer that represents the number you want to perform a right
- /// move on.
- /// @param pos The "pos" parameter represents the number of positions to move the bits to the
- /// right.
- ///
- /// @return the value after performing a right shift operation.
- static int rightMove(int value, int pos)
- {
- if (pos != 0)
- {
- int mask = 0x7fffffff;
- value >>= 1;
- value &= mask;
- value >>= pos - 1;
- }
- return value;
- }
- public class RoiEncoder
- {
- static int HEADER_SIZE = 64;
- static int HEADER2_SIZE = 64;
- static int VERSION = 228; // v1.52t (roi groups, scale stroke width)
- private string path;
- private FileStream f;
- private int polygon = 0, rect = 1, oval = 2, line = 3, freeline = 4, polyline = 5, noRoi = 6, freehand = 7,
- traced = 8, angle = 9, point = 10;
- private byte[] data;
- private string roiName;
- private int roiNameSize;
- private string roiProps;
- private int roiPropsSize;
- private int countersSize;
- private int[] counters;
- private bool subres = true;
-
- /** Creates an RoiEncoder using the specified path. */
- public RoiEncoder(String path)
- {
- this.path = path;
- }
-
- /** Creates an RoiEncoder using the specified OutputStream. */
- public RoiEncoder(FileStream f)
- {
- this.f = f;
- }
-
- /** Saves the specified ROI as a file, returning 'true' if successful. */
- public static bool save(ROI roi, String path)
- {
- RoiEncoder re = new RoiEncoder(path);
- try
- {
- re.write(roi);
- }
- catch (IOException e)
- {
- return false;
- }
- return true;
- }
-
- /** Save the Roi to the file of stream. */
- public void write(ROI roi)
- {
- if (f != null)
- {
- write(roi, f);
- }
- else
- {
- f = new FileStream(path,FileMode.Create);
- write(roi, f);
- f.Close();
- }
- }
-
- /** Saves the specified ROI as a byte array.
- public static byte[] saveAsByteArray(ROI roi)
- {
- if (roi == null) return null;
- byte[] bytes = null;
- try
- {
- MemoryStream outs = new MemoryStream(4096);
- RoiEncoder encoder = new RoiEncoder(path);
- encoder.write(roi);
- outs.close();
- bytes = out.toByteArray();
- }
- catch (IOException e)
- {
- return null;
- }
- return bytes;
- }
- */
- /// The function "write" saves the properties and coordinates of a region of interest (ROI)
- /// to a file stream.
- ///
- /// @param ROI The ROI (Region of Interest) is an object that represents a selected area or
- /// shape in an image. It contains information about the type of ROI (e.g., rectangle,
- /// polygon, line), its position and size, and any additional properties or data associated
- /// with it.
- /// @param FileStream FileStream is a class that represents a stream of bytes that can be
- /// written to a file. It is used to write the data of the ROI (Region of Interest) to a
- /// file.
- ///
- /// @return The code snippet does not have a return statement, so it does not return
- /// anything.
- void write(ROI roi, FileStream f)
- {
- RectangleD r = roi.Rect;
- //if (r.width > 60000 || r.height > 60000 || r.x > 60000 || r.y > 60000)
- // roi.enableSubPixelResolution();
- //int roiType = GetImageJType(roi);
- int type = GetImageJType(roi);
- int options = 0;
- //if (roi.getScaleStrokeWidth())
- // options |= RoiDecoder.SCALE_STROKE_WIDTH;
- roiName = roi.Text;
- if (roiName != null)
- roiNameSize = roiName.Length * 2;
- else
- roiNameSize = 0;
-
- roiProps = roi.properties;
- if (roiProps != null)
- roiPropsSize = roiProps.Length * 2;
- else
- roiPropsSize = 0;
- /*
- switch (roiType) {
- case Roi.POLYGON: type = polygon; break;
- case Roi.FREEROI: type = freehand; break;
- case Roi.TRACED_ROI: type = traced; break;
- case Roi.OVAL: type = oval; break;
- case Roi.LINE: type = line; break;
- case Roi.POLYLINE: type = polyline; break;
- case Roi.FREELINE: type = freeline; break;
- case Roi.ANGLE: type = angle; break;
- case Roi.COMPOSITE: type = rect; break; // shape array size (36-39) will be >0 to indicate composite type
- case Roi.POINT: type = point; break;
- default: type = rect; break;
- }
- */
- /*
- if (roiType == Roi.COMPOSITE) {
- saveShapeRoi(roi, type, f, options);
- return;
- }
- */
- int n = 0;
- int[]
- x = null, y = null;
- float[]
- xf = null, yf = null;
- int floatSize = 0;
- //if (roi instanceof PolygonRoi) {
- //PolygonRoi proi = (PolygonRoi)roi;
- //Polygon p = proi.getNonSplineCoordinates();
- n = roi.PointsD.Count; //p.npoints;
- //x = p.xpoints;
- //y = p.ypoints;
- GetPointsXY(roi, out x, out y);
- if (subres)
- {
- /*
- if (proi.isSplineFit())
- fp = proi.getNonSplineFloatPolygon();
- else
- fp = roi.getFloatPolygon();
- if (n == fp.npoints)
- {
- options |= RoiDecoder.SUB_PIXEL_RESOLUTION;
- if (roi.getDrawOffset())
- options |= RoiDecoder.DRAW_OFFSET;
- xf = fp.xpoints;
- yf = fp.ypoints;
- floatSize = n * 8;
- }
- */
- }
-
-
- countersSize = 0;
- /*
- if (roi instanceof PointRoi) {
- counters = ((PointRoi)roi).getCounters();
- if (counters != null && counters.length >= n)
- countersSize = n * 4;
- }
- */
- data = new byte[HEADER_SIZE + HEADER2_SIZE + n * 4 + floatSize + roiNameSize + roiPropsSize + countersSize];
- data[0] = 73; data[1] = 111; data[2] = 117; data[3] = 116; // "Iout"
- putShort(RoiDecoder.VERSION_OFFSET, VERSION);
- data[RoiDecoder.TYPE] = (byte)type;
- float px, py, pw, ph;
- GetXY(roi, out px, out py);
- GetWH(roi, out pw, out ph);
- putShort(RoiDecoder.TOP, (int)py);
- putShort(RoiDecoder.LEFT, (int)px);
- putShort(RoiDecoder.BOTTOM, (int)(py + ph));
- putShort(RoiDecoder.RIGHT, (int)(px + pw));
- PointD[] pds = roi.GetPoints();
- if (subres && (type == rect || type == oval))
- {
- //FloatPolygon p = null;
- /*
- if (roi instanceof OvalRoi)
- p = ((OvalRoi)roi).getFloatPolygon4();
- else
- {
- int d = roi.getCornerDiameter();
- if (d > 0)
- {
- roi.setCornerDiameter(0);
- p = roi.getFloatPolygon();
- roi.setCornerDiameter(d);
- }
- else
- p = roi.getFloatPolygon();
- }
- */
- if (roi.PointsD.Count == 4)
- {
-
- putFloat(RoiDecoder.XD, (float)pds[0].X);
- putFloat(RoiDecoder.YD, (float)pds[0].Y);
- //putFloat(RoiDecoder.WIDTHD, p.xpoints[1] - roi.PointsD[0]);
- //putFloat(RoiDecoder.HEIGHTD, p.ypoints[2] - p.ypoints[1]);
- putFloat(RoiDecoder.WIDTHD, (float)pds[1].X - (float)pds[0].X);
- putFloat(RoiDecoder.HEIGHTD, (float)pds[2].Y - (float)pds[1].Y);
- options |= RoiDecoder.SUB_PIXEL_RESOLUTION;
- putShort(RoiDecoder.OPTIONS, options);
- }
- }
- if (n > 65535 && type != point)
- {
- if (type == polygon || type == freehand || type == traced)
- {
- //String name = roi.Text;
- //roi = new ShapeRoi(roi);
- //if (name != null) roi.setName(name);
- saveShapeRoi(roi, rect, f, options);
- return;
- }
- //ij.IJ.beep();
- //ij.IJ.log("Non-polygonal selections with more than 65k points cannot be saved.");
- n = 65535;
- }
- if (type == point && n > 65535)
- putInt(RoiDecoder.SIZE, n);
- else
- putShort(RoiDecoder.N_COORDINATES, n);
- putInt(RoiDecoder.POSITION, roi.coord.Z);
-
- /*
- if (type == rect)
- {
- int arcSize = roi.getCornerDiameter();
- if (arcSize > 0)
- putShort(RoiDecoder.ROUNDED_RECT_ARC_SIZE, arcSize);
- }
- */
-
- if(type == line) //(roi instanceof Line)
- {
- //Line line = (Line)roi;
- putFloat(RoiDecoder.X1, (float)pds[0].X);
- putFloat(RoiDecoder.Y1, (float)pds[0].Y);
- putFloat(RoiDecoder.X2, (float)pds[1].X);
- putFloat(RoiDecoder.Y2, (float)pds[1].Y);
- /*
- if (roi instanceof Arrow) {
- putShort(RoiDecoder.SUBTYPE, RoiDecoder.ARROW);
- if (((Arrow)roi).getDoubleHeaded())
- options |= RoiDecoder.DOUBLE_HEADED;
- if (((Arrow)roi).getOutline())
- options |= RoiDecoder.OUTLINE;
- putShort(RoiDecoder.OPTIONS, options);
- putByte(RoiDecoder.ARROW_STYLE, ((Arrow)roi).getStyle());
- putByte(RoiDecoder.ARROW_HEAD_SIZE, (int)((Arrow)roi).getHeadSize());
- } else
- {
- if (roi.getDrawOffset())
- options |= RoiDecoder.SUB_PIXEL_RESOLUTION + RoiDecoder.DRAW_OFFSET;
- }
- */
- }
-
- if (type == point) {
- //PointRoi point = (PointRoi)roi;
- putByte(RoiDecoder.POINT_TYPE, 1);//point.getPointType());
- putShort(RoiDecoder.STROKE_WIDTH, (int)roi.strokeWidth);
- /*
- if (point.getShowLabels())
- options |= RoiDecoder.SHOW_LABELS;
- if (point.promptBeforeDeleting())
- options |= RoiDecoder.PROMPT_BEFORE_DELETING;
- */
- }
-
- if (type == oval)
- {
- /*
- double[] p = null;
- if (roi instanceof RotatedRectRoi) {
- putShort(RoiDecoder.SUBTYPE, RoiDecoder.ROTATED_RECT);
- p = ((RotatedRectRoi)roi).getParams();
- } else
- {
- */
- putShort(RoiDecoder.SUBTYPE, RoiDecoder.ELLIPSE);
- //p = ((EllipseRoi)roi).getParams();
- //}
- float fx, fy, fw, fh;
- GetXY(roi, out fx, out fy);
- GetWH(roi, out fw, out fh);
- putFloat(RoiDecoder.X1, fx);
- putFloat(RoiDecoder.Y1, fy);
- putFloat(RoiDecoder.X2, fw);
- putFloat(RoiDecoder.Y2, fh);
- //putFloat(RoiDecoder.FLOAT_PARAM, (float)p[4]);
- }
-
- // save stroke width, stroke color and fill color (1.43i or later)
- if (VERSION >= 218)
- {
- saveStrokeWidthAndColor(roi);
- /*
- if ((roi instanceof PolygonRoi) && ((PolygonRoi)roi).isSplineFit()) {
- options |= RoiDecoder.SPLINE_FIT;
- putShort(RoiDecoder.OPTIONS, options);
- }
- */
- }
-
- if (roi.type == ROI.Type.Label)//(n == 0 && roi instanceof TextRoi)
- saveTextRoi(roi);
- /*
- else if (n == 0 && roi instanceof ImageRoi)
- options = saveImageRoi((ImageRoi)roi, options);
- */
- //else
- putHeader2(roi, HEADER_SIZE + n * 4 + floatSize);
-
- if (n > 0)
- {
- int base1 = 64;
- int base2 = base1 + 2 * n;
- for (int i = 0; i < n; i++)
- {
- putShort(base1 + i * 2, (int)(x[i] - px));
- putShort(base2 + i * 2, (int)(y[i] - py));
- }
- if (xf != null)
- {
- base1 = 64 + 4 * n;
- base2 = base1 + 4 * n;
- for (int i = 0; i < n; i++)
- {
- putFloat(base1 + i * 4, xf[i]);
- putFloat(base2 + i * 4, yf[i]);
- }
- }
- }
-
- //saveOverlayOptions(roi, options);
- f.Write(data);
- }
-
- /// The function saves the stroke width and color of a region of interest (ROI) in a
- /// specific format.
- ///
- /// @param ROI The ROI parameter is an object that represents a region of interest. It
- /// contains information about the stroke width, stroke color, and fill color of the region.
- void saveStrokeWidthAndColor(ROI roi)
- {
- //BasicStroke stroke = roi.getStroke();
- //if (stroke != null)
- putShort(RoiDecoder.STROKE_WIDTH, (int)roi.strokeWidth);
- Color strokeColor = roi.strokeColor;
- int intColor = (strokeColor.R << 16) | (strokeColor.G << 8) | (strokeColor.B);
- putInt(RoiDecoder.STROKE_COLOR, 0);
- Color fillColor = roi.fillColor;
- int intFillColor = (fillColor.R << 16) | (fillColor.G << 8) | (fillColor.B);
- putInt(RoiDecoder.FILL_COLOR, 0);
- }
-
- /// The function `saveShapeRoi` saves a shape region of interest (ROI) to a file stream in a
- /// specific format.
- ///
- /// @param ROI The `ROI` parameter is an object that represents a region of interest. It
- /// contains information about the shape and position of the region.
- /// @param type The "type" parameter is an integer that represents the type of the ROI. It
- /// is used to determine how the ROI should be saved and interpreted.
- /// @param FileStream FileStream is a class in C# that represents a stream of bytes to read
- /// from or write to a file. It is used to handle file input/output operations. In the given
- /// code, it is used to write the data to a file.
- /// @param options The "options" parameter is an integer that represents various options for
- /// saving the shape ROI. It is used to specify additional information or settings related
- /// to the saving process. The specific meaning and usage of the options parameter would
- /// depend on the context and the implementation of the saveShapeRoi() method.
- void saveShapeRoi(ROI roi, int type, FileStream f, int options)
- {
- //float[] shapeArray = ((ShapeRoi)roi).getShapeAsArray();
- //if (shapeArray == null) return;
- //BufferedOutputStream bout = new BufferedOutputStream(f);
-
- data = new byte[HEADER_SIZE + HEADER2_SIZE + roiNameSize + roiPropsSize];//shapeArray.length * 4 + roiNameSize + roiPropsSize];
- data[0] = 73; data[1] = 111; data[2] = 117; data[3] = 116; // "Iout"
-
- putShort(RoiDecoder.VERSION_OFFSET, VERSION);
- data[RoiDecoder.TYPE] = (byte)type;
-
- float x, y, w, h;
- GetXY(roi, out x,out y);
- GetWH(roi, out w, out h);
- putShort(RoiDecoder.TOP, (int)y);
- putShort(RoiDecoder.LEFT, (int)x);
- putShort(RoiDecoder.BOTTOM, (int)(y + h));
- putShort(RoiDecoder.RIGHT, (int)(x + w));
- putInt(RoiDecoder.POSITION, roi.coord.Z);
- ///putShort(16, n);
- //putInt(36, shapeArray.Length); // non-zero segment count indicate composite type
- if (VERSION >= 218)
- saveStrokeWidthAndColor(roi);
- //saveOverlayOptions(roi, options);
-
- // handle the actual data: data are stored segment-wise, i.e.,
- // the type of the segment followed by 0-6 control point coordinates.
- /*
- int bas = 64;
- for (int i = 0; i < shapeArray.Length; i++)
- {
- putFloat(bas, shapeArray[i]);
- bas += 4;
- }
- */
- int hdr2Offset = HEADER_SIZE;// + shapeArray.Length * 4;
- //ij.IJ.log("saveShapeRoi: "+HEADER_SIZE+" "+shapeArray.length);
- putHeader2(roi, hdr2Offset);
- f.Write(data, 0, data.Length);
- f.Flush();
- }
-
- /*
- void saveOverlayOptions(ROI roi, int options)
- {
- Overlay proto = roi.getPrototypeOverlay();
- if (proto.getDrawLabels())
- options |= RoiDecoder.OVERLAY_LABELS;
- if (proto.getDrawNames())
- options |= RoiDecoder.OVERLAY_NAMES;
- if (proto.getDrawBackgrounds())
- options |= RoiDecoder.OVERLAY_BACKGROUNDS;
- Font font = proto.getLabelFont();
- if (font != null && font.getStyle() == Font.BOLD)
- options |= RoiDecoder.OVERLAY_BOLD;
- if (proto.scalableLabels())
- options |= RoiDecoder.SCALE_LABELS;
- putShort(RoiDecoder.OPTIONS, options);
- }
- */
- /// The function `saveTextRoi` saves the properties of a text region of interest (ROI) into
- /// a byte array.
- ///
- /// @param ROI The `ROI` parameter is an object that represents a region of interest. It
- /// contains information about the font, size, style, text, and other properties of the
- /// region of interest.
- void saveTextRoi(ROI roi)
- {
- //Font font = roi.getCurrentFont();
- string fontName = roi.family;
- int size = (int)roi.fontSize;
- int drawStringMode = 0; //roi.getDrawStringMode() ? 1024 : 0;
- int style = 0;//font.getStyle() + roi.getJustification() * 256 + drawStringMode;
- string text = roi.roiName;
- float angle = 0;
- int angleLength = 4;
- int fontNameLength = fontName.Length;
- int textLength = text.Length;
- int textRoiDataLength = 16 + fontNameLength * 2 + textLength * 2 + angleLength;
- byte[] data2 = new byte[HEADER_SIZE + HEADER2_SIZE + textRoiDataLength + roiNameSize + roiPropsSize];
- Array.Copy(data, 0, data2, 0, HEADER_SIZE);
- data = data2;
- putShort(RoiDecoder.SUBTYPE, RoiDecoder.TEXT);
- putInt(HEADER_SIZE, size);
- putInt(HEADER_SIZE + 4, style);
- putInt(HEADER_SIZE + 8, fontNameLength);
- putInt(HEADER_SIZE + 12, textLength);
- for (int i = 0; i < fontNameLength; i++)
- putShort(HEADER_SIZE + 16 + i * 2, fontName.ElementAt(i));
- for (int i = 0; i < textLength; i++)
- putShort(HEADER_SIZE + 16 + fontNameLength * 2 + i * 2, text.ElementAt(i));
- int hdr2Offset = HEADER_SIZE + textRoiDataLength;
- //ij.IJ.log("saveTextRoi: "+HEADER_SIZE+" "+textRoiDataLength+" "+fontNameLength+" "+textLength);
- putFloat(hdr2Offset - angleLength, angle);
- putHeader2(roi, hdr2Offset);
- }
- /*
- private int saveImageRoi(ROI roi, int options)
- {
- byte[] bytes = roi.getSerializedImage();
- int imageSize = bytes.length;
- byte[] data2 = new byte[HEADER_SIZE + HEADER2_SIZE + imageSize + roiNameSize + roiPropsSize];
- System.arraycopy(data, 0, data2, 0, HEADER_SIZE);
- data = data2;
- putShort(RoiDecoder.SUBTYPE, RoiDecoder.IMAGE);
- for (int i = 0; i < imageSize; i++)
- putByte(HEADER_SIZE + i, bytes[i] & 255);
- int hdr2Offset = HEADER_SIZE + imageSize;
- double opacity = roi.getOpacity();
- putByte(hdr2Offset + RoiDecoder.IMAGE_OPACITY, (int)(opacity * 255.0));
- putInt(hdr2Offset + RoiDecoder.IMAGE_SIZE, imageSize);
- if (roi.getZeroTransparent())
- options |= RoiDecoder.ZERO_TRANSPARENT;
- putHeader2(roi, hdr2Offset);
- return options;
- }
- */
- /// The function "putHeader2" is used to set various properties of a Region of Interest
- /// (ROI) object, such as its position, label color, font size, stroke width, and group.
- ///
- /// @param ROI The ROI parameter is an object of type ROI, which represents a region of
- /// interest in an image. It contains information about the position and size of the ROI, as
- /// well as other properties such as the stroke color, stroke width, and font size.
- /// @param hdr2Offset The `hdr2Offset` parameter is an integer that represents the offset
- /// position in the header where the information for the second header should be stored.
- void putHeader2(ROI roi, int hdr2Offset)
- {
- //ij.IJ.log("putHeader2: "+hdr2Offset+" "+roiNameSize+" "+roiName);
- putInt(RoiDecoder.HEADER2_OFFSET, hdr2Offset);
- putInt(hdr2Offset + RoiDecoder.C_POSITION, roi.coord.C + 1);
- putInt(hdr2Offset + RoiDecoder.Z_POSITION, roi.coord.Z + 1);
- putInt(hdr2Offset + RoiDecoder.T_POSITION, roi.coord.T + 1);
- //Overlay proto = roi.getPrototypeOverlay();
- Color overlayLabelColor = roi.strokeColor; //proto.getLabelColor();
- int intColor = (overlayLabelColor.R << 16) | (overlayLabelColor.G << 8) | (overlayLabelColor.B);
- //if (overlayLabelColor != null)
- putInt(hdr2Offset + RoiDecoder.OVERLAY_LABEL_COLOR, 0);
- //Font font = proto.getLabelFont();
- //if (font != null)
- putShort(hdr2Offset + RoiDecoder.OVERLAY_FONT_SIZE, (int)roi.fontSize);
- if (roiNameSize > 0)
- putName(roi, hdr2Offset);
- double strokeWidth = roi.strokeWidth;
- //if (roi.getStroke() == null)
- // strokeWidth = 0.0;
- putFloat(hdr2Offset + RoiDecoder.FLOAT_STROKE_WIDTH, (float)strokeWidth);
- if (roiPropsSize > 0)
- putProps(roi, hdr2Offset);
- if (countersSize > 0)
- putPointCounters(roi, hdr2Offset);
- putByte(hdr2Offset + RoiDecoder.GROUP, roi.serie);//roi.getGroup());
- }
-
- /// The function "putName" takes a ROI object and an offset value, and sets the name and
- /// length of the ROI in the header.
- ///
- /// @param ROI The ROI parameter is an object of type ROI. It is used to access the
- /// properties and methods of the ROI object within the putName method.
- /// @param hdr2Offset The `hdr2Offset` parameter is an integer value representing the offset
- /// of the header2 in a data structure or file. It is used to calculate the offset for
- /// storing the name of the ROI (Region of Interest) in the data structure or file.
- void putName(ROI roi, int hdr2Offset)
- {
- int offset = hdr2Offset + HEADER2_SIZE;
- int nameLength = roiNameSize / 2;
- putInt(hdr2Offset + RoiDecoder.NAME_OFFSET, offset);
- putInt(hdr2Offset + RoiDecoder.NAME_LENGTH, nameLength);
- for (int i = 0; i < nameLength; i++)
- putShort(offset + i * 2, roiName.ElementAt(i));
- }
-
- /// The function "putProps" takes a ROI object and an offset value, and updates the ROI
- /// properties in the header based on the given offset and ROI object.
- ///
- /// @param ROI The ROI parameter is an object of type ROI. It is used to pass information
- /// about a region of interest.
- /// @param hdr2Offset The `hdr2Offset` parameter is an integer value representing the offset
- /// of the header2 in memory. It is used to calculate the offset for storing the ROI
- /// properties.
- void putProps(ROI roi, int hdr2Offset)
- {
- int offset = hdr2Offset + HEADER2_SIZE + roiNameSize;
- int roiPropsLength = roiPropsSize / 2;
- putInt(hdr2Offset + RoiDecoder.ROI_PROPS_OFFSET, offset);
- putInt(hdr2Offset + RoiDecoder.ROI_PROPS_LENGTH, roiPropsLength);
- for (int i = 0; i < roiPropsLength; i++)
- putShort(offset + i * 2, roiProps.ElementAt(i));
- }
-
- /// The function "putPointCounters" updates the counters in a region of interest (ROI) by
- /// copying the values from an array to a specific offset in memory.
- ///
- /// @param ROI The ROI parameter is an object of type ROI, which likely represents a region
- /// of interest in an image. It may contain information such as the coordinates, size, and
- /// properties of the region.
- /// @param hdr2Offset The `hdr2Offset` parameter is the offset value for the second header
- /// in the data structure. It is used to calculate the position where the point counters
- /// will be stored.
- void putPointCounters(ROI roi, int hdr2Offset)
- {
- int offset = hdr2Offset + HEADER2_SIZE + roiNameSize + roiPropsSize;
- putInt(hdr2Offset + RoiDecoder.COUNTERS_OFFSET, offset);
- for (int i = 0; i < countersSize / 4; i++)
- putInt(offset + i * 4, counters[i]);
- countersSize = 0;
- }
-
- /// The function "putByte" assigns a byte value to a specific index in an array.
- ///
- /// @param bas The parameter "bas" is an integer that represents the base address or index
- /// of the array "data" where the byte value will be stored.
- /// @param v The parameter "v" is an integer value that represents the value to be stored in
- /// the byte array.
- void putByte(int bas, int v)
- {
- data[bas] = (byte)v;
- }
-
- /// The function "putShort" takes two integer parameters, "bas" and "v", and stores the
- /// value of "v" in the "data" array at index "bas" and "bas + 1" after performing a right
- /// shift operation on "v" by 8 bits.
- ///
- /// @param bas The parameter "bas" represents the base index in the "data" array where the
- /// short value will be stored.
- /// @param v The parameter "v" is an integer value that represents the value to be stored in
- /// the data array.
- void putShort(int bas, int v)
- {
- //data[bas] = (byte)(v >>> 8);
- //data[bas] = (byte)UnsignedRightShift(v, 8);
- data[bas] = (byte)rightMove(v, 8);
- data[bas + 1] = (byte)v;
- }
-
- /// The function "putFloat" takes an integer and a float as input and converts the float
- /// into its binary representation, storing it in a byte array.
- ///
- /// @param bas The parameter "bas" represents the base index in the "data" array where the
- /// float value will be stored.
- /// @param v The parameter "v" is a float value that needs to be converted and stored in the
- /// "data" array.
- void putFloat(int bas, float v)
- {
- int tmp = BitConverter.SingleToInt32Bits(v);//Float.floatToIntBits(v);
- data[bas] = (byte)(tmp >> 24);
- data[bas + 1] = (byte)(tmp >> 16);
- data[bas + 2] = (byte)(tmp >> 8);
- data[bas + 3] = (byte)tmp;
- }
-
- /// The function "putInt" takes two integer parameters and stores the bytes of the second
- /// integer in a byte array starting at the specified index in big-endian order.
- ///
- /// @param bas The parameter "bas" represents the base index in the "data" array where the
- /// integer value will be stored.
- /// @param i The parameter "i" is an integer value that needs to be stored in the "data"
- /// array.
- void putInt(int bas, int i)
- {
- data[bas] = (byte)(i >> 24);
- data[bas + 1] = (byte)(i >> 16);
- data[bas + 2] = (byte)(i >> 8);
- data[bas + 3] = (byte)i;
- }
- }
-
- }
-}
diff --git a/Source/Functions.cs b/Source/Functions.cs
index d783129..d2e6fb0 100644
--- a/Source/Functions.cs
+++ b/Source/Functions.cs
@@ -598,7 +598,7 @@ public object PerformFunction(bool imagej)
}
if (FuncType == Function.FunctionType.ImageJ)
{
- Fiji.RunOnImage(script, false, BioConsole.onTab, BioConsole.useBioformats, BioConsole.resultInNewTab);
+ Fiji.RunOnImage(ImageView.SelectedImage,script, false, BioConsole.onTab, BioConsole.useBioformats, BioConsole.resultInNewTab);
}
return null;
}
diff --git a/Source/ImageJ.cs b/Source/ImageJ.cs
deleted file mode 100644
index 8a910aa..0000000
--- a/Source/ImageJ.cs
+++ /dev/null
@@ -1,297 +0,0 @@
-using System;
-using System.Buffers;
-using System.Collections.Generic;
-using System.ComponentModel;
-using System.Linq;
-using System.Text;
-using System.Threading.Tasks;
-using Gtk;
-using ij;
-using ij.plugin;
-using ij.process;
-using BioLib;
-using AForge;
-using java.awt.image;
-
-namespace BioGTK
-{
- public class ImageJ
- {
- static short[] ConvertByteArrayToShortArray(byte[] byteArray, bool littleEndian)
- {
- if (byteArray.Length % 2 != 0)
- {
- throw new ArgumentException("The length of the byte array must be even.");
- }
-
- // Each short is made from two bytes
- short[] shortArray = new short[byteArray.Length / 2];
-
- for (int i = 0; i < shortArray.Length; i++)
- {
- if (littleEndian)
- {
- // If the system is little-endian, reverse the byte order
- shortArray[i] = (short)((byteArray[i * 2 + 1] << 8) | byteArray[i * 2]);
- }
- else
- {
- // If the system is big-endian, keep the byte order as is
- shortArray[i] = (short)((byteArray[i * 2] << 8) | byteArray[i * 2 + 1]);
- }
- }
- return shortArray;
- }
-
- public static ImagePlus GetImagePlus(BioImage bm)
- {
- ImageStack ims = new ImageStack(bm.SizeX, bm.SizeY);
- if (bm.Buffers[0].PixelFormat == AForge.PixelFormat.Format16bppGrayScale)
- {
- // Populate the stack with 16-bit images
- for (int t = 0; t < bm.SizeT; t++)
- {
- for (int c = 0; c < bm.SizeC; c++)
- {
- for (int z = 0; z < bm.SizeZ; z++)
- {
- short[] pixels = ConvertByteArrayToShortArray(bm.Buffers[bm.GetFrameIndex(z, c, t)].Bytes, true);
- ImageProcessor ip = new ShortProcessor(bm.SizeX, bm.SizeY, pixels, java.awt.image.ColorModel.getRGBdefault());
- ims.addSlice("Z" + z + "C" + c + "T" + t, ip);
- }
- }
- }
- }
- else if (bm.Buffers[0].PixelFormat == AForge.PixelFormat.Format8bppIndexed)
- {
- // Create a grayscale IndexColorModel
- byte[] grayscale = new byte[256];
- for (int i = 0; i < 256; i++)
- {
- grayscale[i] = (byte)i;
- }
- IndexColorModel colorModel = new IndexColorModel(8, 256, grayscale, grayscale, grayscale);
- for (int t = 0; t < bm.SizeT; t++)
- {
- for (int c = 0; c < bm.SizeC; c++)
- {
- for (int z = 0; z < bm.SizeZ; z++)
- {
- ImageProcessor ip = new ByteProcessor(bm.SizeX, bm.SizeY, bm.Buffers[bm.GetFrameIndex(z, c, t)].Bytes, colorModel);
- ims.addSlice("Z" + z + "C" + c + "T" + t, ip);
- }
- }
- }
- }
- else if (bm.Buffers[0].PixelFormat == AForge.PixelFormat.Format24bppRgb)
- {
- for (int t = 0; t < bm.SizeT; t++)
- {
- for (int c = 0; c < bm.SizeC; c++)
- {
- for (int z = 0; z < bm.SizeZ; z++)
- {
- byte[] bts = bm.Buffers[bm.GetFrameIndex(z, c, t)].Bytes;
- // Convert the byte array to an int array for the RGB processor
- int[] rgbPixels = new int[bm.SizeX * bm.SizeY];
- for (int i = 0; i < rgbPixels.Length; i++)
- {
- int r = bts[i * 3] & 0xFF; // Red
- int g = bts[i * 3 + 1] & 0xFF; // Green
- int b = bts[i * 3 + 2] & 0xFF; // Blue
- rgbPixels[i] = (r << 16) | (g << 8) | b; // Combine into RGB int
- }
- // Create a ColorProcessor
- ImageProcessor ip = new ColorProcessor(bm.SizeX, bm.SizeY, rgbPixels);
- ims.addSlice("Z" + z + "C" + c + "T" + t, ip);
- }
- }
- }
- }
- else if(bm.Buffers[0].PixelFormat == AForge.PixelFormat.Format32bppArgb || bm.Buffers[0].PixelFormat == AForge.PixelFormat.Format32bppRgb)
- {
- for (int t = 0; t < bm.SizeT; t++)
- {
- for (int c = 0; c < bm.SizeC; c++)
- {
- for (int z = 0; z < bm.SizeZ; z++)
- {
- byte[] bts = bm.Buffers[bm.GetFrameIndex(z, c, t)].Bytes;
- // Convert the byte array to an int array for the ColorProcessor
- int[] rgbaPixels = new int[bm.SizeX * bm.SizeY];
- for (int i = 0; i < rgbaPixels.Length; i++)
- {
- int r = bts[i * 4] & 0xFF; // Red
- int g = bts[i * 4 + 1] & 0xFF; // Green
- int b = bts[i * 4 + 2] & 0xFF; // Blue
- int a = bts[i * 4 + 3] & 0xFF; // Alpha
- rgbaPixels[i] = (a << 24) | (r << 16) | (g << 8) | b; // Combine into ARGB int
- }
- // Create a ColorProcessor with the ARGB int array
- ImageProcessor ip = new ColorProcessor(bm.SizeX, bm.SizeY, rgbaPixels);
- ims.addSlice("Z" + z + "C" + c + "T" + t, ip);
- }
- }
- }
- }
- else if (bm.Buffers[0].PixelFormat == AForge.PixelFormat.Format48bppRgb)
- {
- bm.To16Bit();
- // Populate the stack with 16-bit images
- for (int t = 0; t < bm.SizeT; t++)
- {
- for (int c = 0; c < bm.SizeC; c++)
- {
- for (int z = 0; z < bm.SizeZ; z++)
- {
- short[] pixels = ConvertByteArrayToShortArray(bm.Buffers[bm.GetFrameIndex(z, c, t)].Bytes, true);
- ImageProcessor ip = new ShortProcessor(bm.SizeX, bm.SizeY, pixels, java.awt.image.ColorModel.getRGBdefault());
- ims.addSlice("Z" + z + "C" + c + "T" + t, ip);
- }
- }
- }
- }
- ImagePlus imp = new ImagePlus(bm.ID, ims);
- imp.setDimensions(bm.SizeC, bm.SizeZ, bm.SizeT);
- return imp;
- }
-
- public static bool isRGB(ImagePlus image)
- {
- return image.getType() == ImagePlus.COLOR_RGB;
- }
-
- public static int[] getRGBPixelsFromSlice(ImageStack stack, int sliceIndex)
- {
- // Get the ImageProcessor for the specified slice
- ImageProcessor ip = stack.getProcessor(sliceIndex + 1); // ImageStack uses 1-based indexing
- // Cast to ColorProcessor to access RGB data
- ColorProcessor colorProcessor = (ColorProcessor)ip;
- // Get the RGB pixel data
- return (int[])colorProcessor.getPixels();
- }
- ///
- /// Converts ImagePlus to BioImage.
- ///
- ///
- ///
- ///
- ///
- ///
- /// The BioImage represented by the ImagePlus object.
- public static BioImage GetBioImage(ImagePlus pl, VolumeD vol, double PhysicalX, double PhysicalY, double PhysicalZ)
- {
- BioImage bm = new BioImage(pl.getTitle());
- ImageStack st = pl.getImageStack();
- int b = pl.getBitDepth();
- int slices = pl.getNSlices();
- int chs = pl.getNChannels();
- int frs = pl.getNFrames();
- int rgb = (int)(pl.getBytesPerPixel() * 8);
- bool isrgb = isRGB(pl);
- bm.UpdateCoords(slices,chs,frs,BioImage.Order.TCZ);
- for (int t = 0; t < frs; t++)
- {
- for (int c = 0; c < chs; c++)
- {
- for (int z = 0; z < slices; z++)
- {
- AForge.Bitmap bmp;
- if (!isrgb)
- {
- if (rgb > 8)
- {
- bmp = new AForge.Bitmap(st.getWidth(), st.getHeight(), AForge.PixelFormat.Format16bppGrayScale);
- bm.Buffers.Add(bmp);
- }
- else
- {
- bmp = new AForge.Bitmap(st.getWidth(), st.getHeight(), AForge.PixelFormat.Format8bppIndexed);
- bm.Buffers.Add(bmp);
- }
- }
- else
- {
- bmp = new AForge.Bitmap(st.getWidth(), st.getHeight(), AForge.PixelFormat.Format24bppRgb);
- bm.Buffers.Add(bmp);
- }
- int ind = bm.GetFrameIndex(z, c, t);
- if (!isrgb)
- {
- for (int y = 0; y < pl.getHeight(); y++)
- {
- for (int x = 0; x < pl.getWidth(); x++)
- {
- double d = st.getVoxel(x, y, ind);
- if (bm.Buffers[0].PixelFormat == PixelFormat.Format16bppGrayScale)
- bmp.SetValue(x, y, (ushort)d);
- else if (bm.Buffers[0].PixelFormat == PixelFormat.Format8bppIndexed)
- bmp.SetValue(x, y, (byte)d);
- }
- }
- }
- else
- {
- int[] rgbPixels = getRGBPixelsFromSlice(st, ind);
- // Get the ImageProcessor for the specified slice
- ImageProcessor ip = st.getProcessor(ind + 1); // ImageStack uses 1-based indexing
- // Cast to ColorProcessor to access RGB data
- ColorProcessor colorProcessor = (ColorProcessor)ip;
- for (int y = 0; y < pl.getHeight(); y++)
- {
- for (int x = 0; x < pl.getWidth(); x++)
- {
- int v = colorProcessor.getPixel(x, y);
- int rv = (v >> 16) & 0xFF; // Red
- int gv = (v >> 8) & 0xFF; // Green
- int bv = v & 0xFF; // Blue
- bmp.SetValue(x, y, 0, (byte)rv);
- bmp.SetValue(x, y, 1, (byte)gv);
- bmp.SetValue(x, y, 2, (byte)bv);
- }
- }
-
- }
- }
- }
- }
- for(int t = 0;t < chs; t++)
- {
- if(isrgb)
- bm.Channels.Add(new AForge.Channel(t, rgb, 3));
- else
- bm.Channels.Add(new AForge.Channel(t, rgb, 1));
- if (t == 0)
- {
- bm.rgbChannels[0] = 0;
- }
- else
- if (t == 1)
- {
- bm.rgbChannels[1] = 1;
- }
- else
- if (t == 2)
- {
- bm.rgbChannels[2] = 2;
- }
- }
- bm.Resolutions.Add(new Resolution(pl.getWidth(), pl.getHeight(), bm.Buffers[0].PixelFormat, PhysicalX, PhysicalY, PhysicalZ, vol.Location.X, vol.Location.Y, vol.Location.X));
- bm.Volume = vol;
- bm.littleEndian = BitConverter.IsLittleEndian;
- bm.seriesCount = 1;
- bm.bitsPerPixel = b;
- BioImage.AutoThreshold(bm, true);
- if (rgb > 8)
- bm.StackThreshold(true);
- else
- bm.StackThreshold(false);
-
- if (bm.RGBChannelCount == 4)
- {
- bm.Channels.Last().SamplesPerPixel = 4;
- }
- return bm;
- }
- }
-}
diff --git a/Source/ImageView.cs b/Source/ImageView.cs
index 2f5ff2b..f58e508 100644
--- a/Source/ImageView.cs
+++ b/Source/ImageView.cs
@@ -581,13 +581,47 @@ private static SKImage Convert32bppBitmapToSKImage(Bitmap sourceBitmap)
SKBitmap skBitmap = new SKBitmap(width, height, SKColorType.Bgra8888, SKAlphaType.Opaque);
- BitmapData bitmapData = sourceBitmap.LockBits(new Rectangle(0, 0, width, height), ImageLockMode.ReadOnly, PixelFormat.Format32bppArgb);
+ BitmapData bitmapData = sourceBitmap.LockBits(new Rectangle(0, 0, width, height), ImageLockMode.ReadOnly, sourceBitmap.PixelFormat);
unsafe
{
byte* sourcePtr = (byte*)bitmapData.Scan0.ToPointer();
byte* destPtr = (byte*)skBitmap.GetPixels().ToPointer();
+ for (int y = 0; y < height; y++)
+ {
+ for (int x = 0; x < width; x++)
+ {
+ destPtr[0] = sourcePtr[0]; // Blue
+ destPtr[1] = sourcePtr[1]; // Green
+ destPtr[2] = sourcePtr[2]; // Red
+ destPtr[3] = 255; // Alpha (fully opaque)
+
+ sourcePtr += 4;
+ destPtr += 4;
+ }
+ }
+ }
+
+ sourceBitmap.UnlockBits(bitmapData);
+
+ return SKImage.FromBitmap(skBitmap);
+ }
+ public static SKImage Convert16bppBitmapToSKImage(Bitmap sourceBitmap)
+ {
+ Bitmap bm = sourceBitmap.GetImageRGB();
+ int width = bm.Width;
+ int height = bm.Height;
+
+ SKBitmap skBitmap = new SKBitmap(width, height, SKColorType.Bgra8888, SKAlphaType.Opaque);
+
+ BitmapData bitmapData = sourceBitmap.LockBits(new Rectangle(0, 0, width, height), ImageLockMode.ReadOnly, bm.PixelFormat);
+
+ unsafe
+ {
+ byte* sourcePtr = (byte*)bm.Data.ToPointer();
+ byte* destPtr = (byte*)skBitmap.GetPixels().ToPointer();
+
for (int y = 0; y < height; y++)
{
for (int x = 0; x < width; x++)
@@ -614,9 +648,9 @@ public static SKImage BitmapToSKImage(AForge.Bitmap bitm)
if (bitm.PixelFormat == PixelFormat.Format32bppArgb)
return Convert32bppBitmapToSKImage(bitm);
if (bitm.PixelFormat == PixelFormat.Format16bppGrayScale)
- return Convert32bppBitmapToSKImage(bitm.GetImageRGBA());
+ return Convert16bppBitmapToSKImage(bitm.GetImageRGB());
if (bitm.PixelFormat == PixelFormat.Format48bppRgb)
- return Convert32bppBitmapToSKImage(bitm.GetImageRGBA());
+ return Convert16bppBitmapToSKImage(bitm.GetImageRGB());
else
throw new NotSupportedException("PixelFormat " + bitm.PixelFormat + " is not supported for SKImage.");
}
@@ -1946,6 +1980,7 @@ public List GetSelectedROIs()
/// @param MotionNotifyEventArgs
private void ImageView_MotionNotifyEvent(object o, MotionNotifyEventArgs e)
{
+ UpdateView(true, false);
App.viewer = this;
Modifiers = e.Event.State;
MouseMove = new PointD(e.Event.X,e.Event.Y);
diff --git a/Source/NodeView.cs b/Source/NodeView.cs
index 7c15830..ca0ec0e 100644
--- a/Source/NodeView.cs
+++ b/Source/NodeView.cs
@@ -47,7 +47,6 @@ public static NodeView Create(string[] args)
/* The code you provided is the constructor for the `NodeView` class. */
protected NodeView(Builder builder, IntPtr handle, string[] args) : base(handle)
{
- Console.WriteLine("Creating Nodeview.");
_builder = builder;
builder.Autoconnect(this);
string st = System.IO.Path.GetDirectoryName(Environment.ProcessPath);
@@ -59,7 +58,7 @@ protected NodeView(Builder builder, IntPtr handle, string[] args) : base(handle)
System.IO.Directory.CreateDirectory(st + "/Plugins");
System.IO.Directory.CreateDirectory(st + "/Models");
App.nodeView = this;
- App.Initialize(true);
+ App.Initialize();
SetupHandlers();
Console.WriteLine("Parsing arguments.");
if (args != null)
@@ -70,12 +69,15 @@ protected NodeView(Builder builder, IntPtr handle, string[] args) : base(handle)
}
foreach (string item in args)
{
- BioImage.OpenAsync(item, false, true, true, 0);
+ BioImage.OpenAsync(item, false, true, true, 0).Wait();
+ BioImage bm = Images.GetImage(item);
+ App.tabsView.AddTab(bm);
}
}
Console.WriteLine("Initializing nodes.");
InitItems();
App.ApplyStyles(this);
+ Console.WriteLine("NodeView initialized.");
}
/// It takes a list of images, and for each image, it takes a list of bitmaps, and for each
diff --git a/Source/Scripting.cs b/Source/Scripting.cs
index 5bfddc3..819683b 100644
--- a/Source/Scripting.cs
+++ b/Source/Scripting.cs
@@ -231,7 +231,7 @@ public static void Run(Script rn)
private static string scriptName = "";
private static string str = "";
/// It runs a script in a separate thread
- private static void RunScript()
+ private static async void RunScript()
{
Script rn = scripts[scriptName];
rn.ex = null;
@@ -240,7 +240,10 @@ private static void RunScript()
try
{
rn.done = false;
- Fiji.RunString(rn.scriptString,"", false);
+ if (App.UseFiji)
+ await Fiji.RunStringFiji(ImageView.SelectedImage,rn.scriptString, "", false);
+ else
+ ImageJ.RunString(rn.scriptString, "", false);
rn.done = true;
}
catch (Exception e)
@@ -678,7 +681,10 @@ private void runButton_Click(object sender, ButtonPressEventArgs args)
{
if (scriptLabel.Text.EndsWith(".ijm"))
{
- Fiji.RunString(view.Buffer.Text, ImageView.SelectedImage.ID, headlessBox.Active);
+ if (App.UseFiji)
+ Fiji.RunStringFiji(ImageView.SelectedImage,view.Buffer.Text, ImageView.SelectedImage.ID, headlessBox.Active);
+ else
+ ImageJ.RunString(view.Buffer.Text, ImageView.SelectedImage.ID, headlessBox.Active);
}
else
Run();
diff --git a/Source/Search.cs b/Source/Search.cs
index b2e1eae..6397e21 100644
--- a/Source/Search.cs
+++ b/Source/Search.cs
@@ -69,7 +69,7 @@ private void TreeView_RowActivated(object o, RowActivatedArgs args)
string itemName = (string)treeView.Model.GetValue(iter, 0);
if(!itemName.EndsWith(".txt") || !itemName.EndsWith(".ijm") && !itemName.EndsWith(".cs"))
{
- Fiji.RunOnImage("run(\"" + itemName + "\")",BioConsole.headless,BioConsole.onTab,BioConsole.useBioformats,BioConsole.resultInNewTab);
+ Fiji.RunOnImage(ImageView.SelectedImage,"run(\"" + itemName + "\")",BioConsole.headless,BioConsole.onTab,BioConsole.useBioformats,BioConsole.resultInNewTab);
}
else
Scripting.RunByName(itemName);
diff --git a/Source/Settings.cs b/Source/Settings.cs
deleted file mode 100644
index 9fff9a9..0000000
--- a/Source/Settings.cs
+++ /dev/null
@@ -1,65 +0,0 @@
-using System;
-using System.Collections.Generic;
-using System.Linq;
-using System.Text;
-using System.Threading.Tasks;
-using System.IO;
-
-namespace BioGTK
-{
- public static class Settings
- {
- /* Creating a new dictionary with a string as the key and a string as the value. */
- static Dictionary Default = new Dictionary();
- /// If the dictionary contains the key, return the value, otherwise return an empty string
- ///
- /// @param name The name of the setting you want to get.
- ///
- /// @return The value of the key in the dictionary.
- public static string GetSettings(string name)
- {
- if (Default.Keys.Count == 0)
- {
- Load();
- }
- if (Default.ContainsKey(name)) return Default[name];
- return "";
- }
- /// It adds a new setting to the settings file
- ///
- /// @param name The name of the setting.
- /// @param val The value of the setting
- public static void AddSettings(string name,string val)
- {
- if (Default.ContainsKey(name))
- Default[name] = val;
- else
- Default.Add(name, val);
- }
- static string path = System.IO.Path.GetDirectoryName(Environment.ProcessPath);
- /// It takes the values in the dictionary and writes them to a file
- public static void Save()
- {
- string val = "";
- foreach (var item in Default)
- {
- val += item.Key + "=" + item.Value + Environment.NewLine;
- }
- File.WriteAllText(path + "/Settings.txt", val);
- }
- /// It reads a file and adds the contents to a dictionary
- ///
- /// @return The settings are being returned.
- public static void Load()
- {
- if (!File.Exists(path + "/Settings.txt"))
- return;
- string[] sts = File.ReadAllLines(path + "/Settings.txt");
- foreach (string item in sts)
- {
- string[] st = item.Split('=');
- Default.Add(st[0], st[1]);
- }
- }
- }
-}
diff --git a/Source/TabsView.cs b/Source/TabsView.cs
index 75d3ecb..60ec0dc 100644
--- a/Source/TabsView.cs
+++ b/Source/TabsView.cs
@@ -1,8 +1,9 @@
using AForge;
using Bio;
using Gtk;
+using ij.plugin.filter;
using ikvm.runtime;
-using loci.formats.gui;
+using org.checkerframework.checker.initialization.qual;
using System;
using System.Collections.Generic;
using System.ComponentModel;
@@ -181,11 +182,6 @@ protected TabsView(Builder builder, IntPtr handle) : base(handle)
App.tabsView = this;
builder.Autoconnect(this);
filteredMenu.Active = true;
- //If the platform is MacOS we need to use Fiji/ImageJ without using IKVM.
- if (RuntimeInformation.IsOSPlatform(OSPlatform.OSX))
- {
- App.UseFiji = true;
- }
SetupHandlers();
progress = Progress.Create(title, "", "");
Function.InitializeMainMenu();
@@ -234,7 +230,7 @@ protected TabsView(Builder builder, IntPtr handle) : base(handle)
mi.ButtonPressEvent += Mi_ButtonPressEvent;
rm.Append(mi);
}
- foreach (Fiji.Macro.Command c in Fiji.Macros)
+ foreach (Fiji.Macro.Command c in BioLib.Fiji.Macro.Commands.Values)
{
MenuItem mi = new MenuItem(c.Name);
mi.ButtonPressEvent += Mi_ButtonPressEvent;
@@ -245,15 +241,43 @@ protected TabsView(Builder builder, IntPtr handle) : base(handle)
Plugins.Initialize();
ML.ML.Initialize();
}
-
+ /// This function creates a file chooser dialog that allows the user to select the location of
+ /// the ImageJ executable
+ ///
+ /// @return A boolean value.
+ public static bool SetImageJPath()
+ {
+ string st = BioLib.Settings.GetSettings("ImageJPath");
+ if (st != "")
+ {
+ Fiji.ImageJPath = BioLib.Settings.GetSettings("ImageJPath");
+ return true;
+ }
+ string title = "Select ImageJ Executable Location";
+ if (OperatingSystem.IsMacOS())
+ title = "Select ImageJ Executable Location (Fiji.app/Contents/MacOS/ImageJ-macosx)";
+ Gtk.FileChooserDialog filechooser =
+ new Gtk.FileChooserDialog(title, Scripting.window,
+ FileChooserAction.Open,
+ "Cancel", ResponseType.Cancel,
+ "Save", ResponseType.Accept);
+ filechooser.SetCurrentFolder(System.IO.Path.GetDirectoryName(Environment.ProcessPath));
+ if (filechooser.Run() != (int)ResponseType.Accept)
+ return false;
+ Fiji.ImageJPath = filechooser.Filename;
+ BioLib.Settings.AddSettings("ImageJPath", filechooser.Filename);
+ filechooser.Destroy();
+ BioLib.Settings.Save();
+ return true;
+ }
private void Mi_ButtonPressEvent(object o, ButtonPressEventArgs args)
{
MenuItem m = (MenuItem)o;
if (m.Label.EndsWith(".ijm") || m.Label.EndsWith(".txt") && !m.Label.EndsWith(".cs"))
{
- string file = Fiji.ImageJMacroPath + m.Label;
+ string file = Fiji.ImageJPath + m.Label;
string ma = File.ReadAllText(file);
- Fiji.RunOnImage(ma, BioConsole.headless, BioConsole.onTab, BioConsole.useBioformats, BioConsole.resultInNewTab);
+ Fiji.RunOnImage(ImageView.SelectedImage,ma, BioConsole.headless, BioConsole.onTab, BioConsole.useBioformats, BioConsole.resultInNewTab);
}
else
Scripting.RunByName(m.Label);
@@ -268,22 +292,26 @@ private void Mi_ButtonPressEvent(object o, ButtonPressEventArgs args)
recentMenu.ShowAll();
}
- private void CommandMenuItem_ButtonPressEvent(object o, ButtonPressEventArgs args)
+ private async void CommandMenuItem_ButtonPressEvent(object o, ButtonPressEventArgs args)
{
if (ImageView.SelectedImage == null) return;
MenuItem m = (MenuItem)o;
- Fiji.RunOnImage("run(\"" + m.Label + "\");", BioConsole.headless, BioConsole.onTab, BioConsole.useBioformats, BioConsole.resultInNewTab);
+ BioImage bm = await Fiji.RunOnImage(ImageView.SelectedImage, "run(\"" + m.Label + "\");", BioConsole.headless, BioConsole.onTab, BioConsole.useBioformats, BioConsole.resultInNewTab);
MenuItem mi = new MenuItem(m.Label);
mi.ButtonPressEvent += CommandMenuItem_ButtonPressEvent;
bool con = false;
foreach (MenuItem item in recent.Children)
{
if (item.Label == m.Label)
+ {
con = true;
+ break;
+ }
}
if(!con)
recent.Append(mi);
recentMenu.ShowAll();
+ AddTab(bm);
}
/// When the user clicks on a menu item, the selected image is rotated or flipped according to
@@ -570,7 +598,7 @@ private void ExportROIsFromImageJMenu_ButtonPressEvent(object o, ButtonPressEven
{
f = f.Replace(".roi","") + i + ".roi";
}
- Fiji.RoiEncoder.save(item, f);
+ Fiji.RoiEncoder.save(ImageView.SelectedImage, item, f);
i++;
}
filechooser.Hide();
@@ -596,7 +624,7 @@ private void ImportROIsFromImageJMenu_ButtonPressEvent(object o, ButtonPressEven
return;
foreach (string item in filechooser.Filenames)
{
- ROI roi = Fiji.RoiDecoder.open(item);
+ ROI roi = Fiji.RoiDecoder.open(item, ImageView.SelectedImage.PhysicalSizeX, ImageView.SelectedImage.PhysicalSizeY, ImageView.SelectedImage.Volume.Location.X, ImageView.SelectedImage.Volume.Location.Y);
ImageView.SelectedImage.Annotations.Add(roi);
}
filechooser.Hide();
@@ -710,13 +738,24 @@ private void RgbMenu_ButtonPressEvent(object o, ButtonPressEventArgs args)
/// @param BioImage This is the image that you want to display.
public void AddTab(BioImage im)
{
- ImageView v = ImageView.Create(im);
- viewers.Add(v);
- v.Show();
- Label dummy = new Gtk.Label(System.IO.Path.GetDirectoryName(im.file) + "/" + im.Filename);
- dummy.Visible = false;
- tabsView.AppendPage(dummy, new Gtk.Label(im.Filename));
- tabsView.ShowAll();
+ try
+ {
+ Application.Invoke(delegate
+ {
+ ImageView v = ImageView.Create(im);
+ viewers.Add(v);
+ v.Show();
+ Label dummy = new Gtk.Label(System.IO.Path.GetDirectoryName(im.file) + "/" + im.Filename);
+ dummy.Visible = false;
+ tabsView.AppendPage(dummy, new Gtk.Label(im.Filename));
+ tabsView.ShowAll();
+ Console.WriteLine("New tab added for " + im.Filename);
+ });
+ }
+ catch (Exception e)
+ {
+ Console.WriteLine(e.ToString());
+ }
}
/// When the TabsView is focused, set the tabsView variable in the App class to the TabsView
@@ -892,6 +931,7 @@ private static void ProgressUpdate()
}
private static void StartProgress(string titl, string status)
{
+ done = false;
title = titl;
BioImage.Progress = 0;
progress.Status = status;
diff --git a/Source/Updater.cs b/Source/Updater.cs
index e207f4b..ed6e973 100644
--- a/Source/Updater.cs
+++ b/Source/Updater.cs
@@ -69,7 +69,7 @@ protected Updater(Builder builder, IntPtr handle) : base(handle)
builder.Autoconnect(this);
this.DeleteEvent += Updater_DeleteEvent;
upBut.ButtonPressEvent += UpButton_ButtonPressEvent;
- string st = Settings.GetSettings("UpdateSites");
+ string st = BioLib.Settings.GetSettings("UpdateSites");
if(st!="")
{
string[] ups = st.Split(',');
@@ -122,8 +122,8 @@ private void Updater_DeleteEvent(object o, DeleteEventArgs args)
else
ups += sts[i];
}
- Settings.AddSettings("UpdateSites", ups);
- Settings.Save();
+ BioLib.Settings.AddSettings("UpdateSites", ups);
+ BioLib.Settings.Save();
}
public static async Task DownloadFileAsync(string fileUrl, string savePath)
{
diff --git a/macro-commands.csv b/macro-commands.csv
deleted file mode 100644
index 399cddb..0000000
--- a/macro-commands.csv
+++ /dev/null
@@ -1,815 +0,0 @@
-16-bit,ij.plugin.Converter("16-bit")
-2D Histogram,util.Histogram_2D
-2D Stitching,Stitching_2D
-3-3-2 RGB,ij.plugin.LutLoader("3-3-2 RGB")
-32-bit,ij.plugin.Converter("32-bit")
-3D Objects Counter,_3D_objects_counter
-3D OC Options,_3D_OC_Options
-3D Project...,ij.plugin.Projector
-3D Stitching,Stitching_3D
-3D Surface Plot,Interactive_3D_Surface_Plot
-3D Viewer,ij3d.ImageJ_3D_Viewer
-8-bit,ij.plugin.Converter("8-bit")
-8-bit Color,ij.plugin.Converter("8-bit Color")
-About bUnwarpJ...,bunwarpj.Credits
-About ImageJ...,ij.plugin.AboutBox
-About This Submenu...,ij.plugin.SimpleCommands("about")
-About TrakEM2...,ini.trakem2.utils.Utils
-About...,QuickPALM.Run_MyMacro("About_.txt")
-About/Help LSMToolbox,LSM_Toolbox("about")
-Abs,ij.plugin.filter.ImageMath("abs")
-Add Empty Frame,video2.Add_Empty_Frame
-Add Image...,ij.plugin.OverlayCommands("image")
-Add Noise,ij.plugin.filter.Filters("add")
-Add Popup Split Channels,script:Examples/Add_Popup_Split_Channels.bsh
-Add Shortcut by Name... ,ij.plugin.Hotkeys("install2")
-Add Shortcut... ,ij.plugin.Hotkeys("install")
-Add Slice,ij.plugin.StackEditor("add")
-Add Specified Noise...,ij.plugin.filter.Filters("noise")
-Add...,ij.plugin.filter.ImageMath("add")
-Adelsons Squares,script:File/Open_Samples/Adelsons_Squares.ijm
-Advanced Weka Segmentation,trainableSegmentation.Weka_Segmentation
-Align Image by line ROI,Align_Image
-Amira as TrakEM2...,ini.trakem2.New_Project("amira")
-Amira...,AmiraMeshReader_
-AmiraMesh ...,AmiraMeshWriter_
-AmiraTable ...,AmiraTableWriter_
-Anaglyph for Red Cyan glasses,script:Examples/Anaglyph_for_Red_Cyan_glasses.rb
-Analyse Particles,QuickPALM.Analyse_Particles
-Analyze Line Graph,ij.plugin.filter.LineGraphAnalyzer
-Analyze Particles...,ij.plugin.filter.ParticleAnalyzer
-Analyze Skeleton (2D/3D),sc.fiji.analyzeSkeleton.AnalyzeSkeleton_
-Analyze...,sc.fiji.io.Analyze_Reader
-Analyze... ,sc.fiji.io.Analyze_Writer
-AND...,ij.plugin.filter.ImageMath("and")
-Animated Gif ... ,sc.fiji.io.Gif_Stack_Writer
-Animated Gif...,sc.fiji.io.Animated_Gif_Reader
-Animation Options...,ij.plugin.Animator("options")
-Anisotropic Diffusion 2D,anisotropic_diffusion.Anisotropic_Diffusion_2D
-Appearance...,ij.plugin.AppearanceOptions
-Apply external transformation,fiji.plugin.Apply_External_Transformation
-Apply LUT,ij.plugin.filter.LutApplier
-Apply saved SIOX segmentator,siox.Load_Segmentation
-Apply Transformations,spim.fiji.plugin.Apply_Transformation
-Area to Line,ij.plugin.Selection("toline")
-Arrange Channels...,ij.plugin.ChannelArranger
-Arrow ,fiji.util.ArrowTool
-Arrow Tool...,ij.plugin.ArrowToolOptions
-As HDF5,spim.fiji.plugin.resave.Resave_HDF5
-As TIFF,spim.fiji.plugin.resave.Resave_TIFF
-Attach to Cluster...,edu.utexas.clm.archipelago.Fiji_Archipelago("client")
-AuPbSn 40,ij.plugin.URLOpener("AuPbSn40.jpg")
-Auto Crop,fiji.selection.Select_Bounding_Box("autocrop")
-Auto Crop (guess background color),fiji.selection.Select_Bounding_Box("autoautocrop")
-Auto Local Threshold,fiji.threshold.Auto_Local_Threshold
-Auto Threshold,fiji.threshold.Auto_Threshold
-Average Color,Average_Color
-Average Images,vib.Average_Images
-AVI...,ij.plugin.AVI_Reader
-AVI... ,ij.plugin.filter.AVI_Writer
-Balloon,sc.fiji.balloonSegmentation.BalloonSegmentation_
-Bandpass Filter...,ij.plugin.filter.FFTFilter
-Bat Cochlea Renderings,ij.plugin.URLOpener("bat-cochlea-renderings.zip")
-Bat Cochlea Volume,ij.plugin.URLOpener("bat-cochlea-volume.zip")
-Bead-based registration,fiji.plugin.Bead_Registration
-Benchmark,ij.plugin.Benchmark
-Big Warp,bdv.ij.BigWarpImagePlusPlugIn
-Big Warp Apply,bdv.ij.ApplyBigwarpPlugin
-Big Warp to Displacement field,bdv.ij.BigWarpToDeformationFieldPlugIn
-Big Warp XML/HDF5,command:bdv.ij.BigWarpBdvCommand
-BigDataViewer...,command:bdv.ij.ImportPlugIn
-Bilateral Filter,Bilateral_Filter
-Bin...,ij.plugin.Binner
-Bio-Formats,loci.plugins.LociImporter("location=[Local machine] windowless=false ")
-Bio-Formats (Remote),loci.plugins.LociImporter("location=[Internet]")
-Bio-Formats (Windowless),loci.plugins.LociImporter("location=[Local machine] windowless=true ")
-Bio-Formats Exporter,loci.plugins.LociExporter("")
-Bio-Formats Importer,loci.plugins.LociImporter("location=[Local machine] windowless=false ")
-Bio-Formats Macro Extensions,loci.plugins.macro.LociFunctions("")
-Bio-Formats Plugins Configuration,loci.plugins.config.LociConfig("")
-Bio-Formats Plugins...,loci.plugins.About("")
-Bio-Formats Remote Importer,loci.plugins.LociImporter("location=[Internet]")
-Bio-Formats Windowless Importer,loci.plugins.LociImporter("location=[Local machine] windowless=true ")
-Biorad ...,Biorad_Writer
-Biorad...,Biorad_Reader
-Bleach Correction,emblcmci.BleachCorrection
-blend two images,script:Examples/blend_two_images.clj
-Blobs Demo in Ruby,script:Examples/Blobs_Demo_in_Ruby.rb
-Blow/Lasso Tool,plugin.Lasso_
-Blue,ij.plugin.LutLoader("blue")
-BMP...,ij.plugin.filter.Writer("bmp")
-Boats,ij.plugin.URLOpener("boats.gif")
-Bridge (174K),ij.plugin.URLOpener("bridge.gif")
-Browse BigDataServer,command:bdv.ij.BigDataBrowserPlugIn
-bUnwarpJ,bunwarpj.bUnwarpJ_
-Cache Sample Images ,ij.plugin.URLOpener("cache")
-Calculator Plus,Calculator_Plus
-Calibrate...,ij.plugin.filter.Calibrator
-Calibration Bar...,ij.plugin.CalibrationBar
-Canvas Size...,ij.plugin.CanvasResizer
-Capture Delayed...,ij.plugin.ScreenGrabber("delay")
-Capture Image,ij.plugin.ScreenGrabber("image")
-Cardio (RGB DICOM),ij.plugin.URLOpener("cardio.dcm.zip")
-Cascade,ij.plugin.WindowOrganizer("cascade")
-Cell Colony,ij.plugin.URLOpener("Cell_Colony.jpg")
-Cell Counter,sc.fiji.cellCounter.Cell_Counter
-celsius to fahrenheit,script:Examples/celsius_to_fahrenheit.clj
-Centipede Drawing (45KB),ij.plugin.URLOpener("http://imagej.net/media/centipede-drawing.jpg")
-Centipede Mivart (43KB),ij.plugin.URLOpener("http://imagej.net/media/centipede-mivart.png")
-Check Required Update Sites,script:Plugins/AutoRun/Check_Required_Update_Sites.js
-chess ,script:Examples/chess_.py
-Circle Interpolator,sc.fiji.timelapse.Circle_Interpolator
-Clear,ij.plugin.filter.Filler("clear")
-Clear Outside,ij.plugin.filter.Filler("outside")
-Clear Results,ij.plugin.filter.Analyzer("clear")
-Close-,ij.plugin.filter.Binary("close")
-Clown,ij.plugin.URLOpener("clown.jpg")
-Collect Garbage,CollectGarbage_
-Coloc 2,sc.fiji.coloc.Coloc_2
-Colocalization Test,sc.fiji.coloc.Colocalisation_Test
-Colocalization Threshold,sc.fiji.coloc.Colocalisation_Threshold
-Colocalize...,command:net.imagej.ops.commands.coloc.Colocalize
-Color Balance...,ij.plugin.frame.ContrastAdjuster("balance")
-Color Clustering,trainableSegmentation.unsupervised.Color_Clustering
-Color Histogram,ColorHistogram_
-Color Histogram...,ColorHistogram_("about")
-Color Inspector 3D,Color_Inspector_3D
-Color Threshold...,ij.plugin.frame.ColorThresholder
-Colors...,ij.plugin.Colors
-Colour Deconvolution,sc.fiji.colourDeconvolution.Colour_Deconvolution
-Combine Profile Stacks,sc.fiji.timelapse.Combine_Profile_Stacks
-Combine...,ij.plugin.StackCombiner
-Command Launcher BeanShell,script:Examples/Command_Launchers/Command_Launcher_BeanShell.bsh
-Command Launcher Clojure,script:Examples/Command_Launchers/Command_Launcher_Clojure.clj
-Command Launcher Javascript,script:Examples/Command_Launchers/Command_Launcher_Javascript.js
-Command Launcher Python,script:Examples/Command_Launchers/Command_Launcher_Python.py
-Command Launcher Ruby,script:Examples/Command_Launchers/Command_Launcher_Ruby.rb
-Comparing Lengths,script:File/Open_Samples/Comparing_Lengths.ijm
-Compile and Run...,sc.fiji.compat.Compile_and_Run
-Compiler...,ij.plugin.Compiler("options")
-compose rgb-stacks,script:Examples/compose_rgb-stacks.bsh
-Compute Curvatures,Compute_Curvatures
-Compute Topography,Compute_Topography
-Concatenate...,ij.plugin.Concatenator
-Confocal Series,ij.plugin.URLOpener("confocal-series.zip")
-Console,command:org.scijava.ui.swing.console.ShowConsole
-Conversions...,ij.plugin.Options("conv")
-Convert to Mask,ij.plugin.Thresholder("mask")
-Convert...,ij.plugin.BatchConverter
-Convex Hull,ij.plugin.Selection("hull")
-Convolve (3D),process3d.Convolve_3d
-Convolve...,ij.plugin.filter.Convolver
-Coordinates...,ij.plugin.Coordinates
-Copy to System,ij.plugin.Clipboard("scopy")
-Correct 3D drift,script:Plugins/Registration/Correct_3D_drift.py
-Cover Maker,script:Examples/CoverMaker/Cover_Maker.py
-CPU Meter,CPU_Meter
-Create Desktop Icon,script:Plugins/Utilities/Create_Desktop_Icon.bsh
-Create Mask,ij.plugin.Selection("mask")
-Create Selection,ij.plugin.Selection("from")
-Crop (3D),stacks.Three_Pane_Crop
-CT (16-bit DICOM),ij.plugin.URLOpener("ct.dcm.zip")
-Curve Fitting...,ij.plugin.frame.Fitter
-Custom Filter...,ij.plugin.filter.FFTCustomFilter
-Cyan,ij.plugin.LutLoader("cyan")
-DAT EMMENU ...,sc.fiji.io.Open_DAT_EMMENU
-Define Bounding Box,spim.fiji.plugin.Define_Bounding_Box
-Define Multi-View Dataset,spim.fiji.plugin.Define_Multi_View_Dataset
-Deinterleave,DeInterleave_
-Delaunay Voronoi,Delaunay_Voronoi
-Delayed Snapshot,script:Examples/Delayed_Snapshot.py
-Delayed Snapshot Window,script:Examples/Delayed_Snapshot_Window.bsh
-Delete Frame,video2.Delete_Frame
-Delete Slice,ij.plugin.StackEditor("delete")
-Despeckle,ij.plugin.filter.RankFilters("despeckle")
-Dev. Resources...,ij.plugin.BrowserLauncher("http://imagej.net/ij/developer/index.html")
-DF3 ...,sc.fiji.io.Save_DF3
-DF3...,sc.fiji.io.Open_DF3
-Dialog Prompt Demo,command:org.scijava.ui.swing.commands.DialogPromptDemo
-Dichromacy,Dichromacy_
-DICOM...,ij.plugin.Options("dicom")
-Dilate,ij.plugin.filter.Binary("dilate")
-Dilate (3D),process3d.Dilate_
-Directionality,fiji.analyze.directionality.Directionality_
-Display LUTs,ij.plugin.SimpleCommands("display")
-Display View,spim.fiji.plugin.Display_View
-Distance Map,ij.plugin.filter.EDM("edm")
-Distance Map to Distance Ridge,sc.fiji.localThickness.Distance_Ridge
-Distance Ridge to Local Thickness,sc.fiji.localThickness.Local_Thickness_Parallel
-Distance Transform 3D,process3d.Distance_Transform_3D
-Distortion Correction,lenscorrection.Distortion_Correction
-Distribution...,ij.plugin.Distribution
-Divide...,ij.plugin.filter.ImageMath("div")
-DM3 Reader...,sc.fiji.io.DM3_Reader
-Dot Blot,ij.plugin.URLOpener("Dot_Blot.jpg")
-downsample ,script:Examples/downsample_.js
-Draw Roi,video2.Draw_Roi
-Dump Stack,command:org.scijava.plugins.commands.debug.DumpStack
-Duplicate,sc.fiji.i5d.plugin.Duplicate_Image5D("")
-Duplicate Frame,video2.Duplicate_Frame
-Duplicate Transformations,spim.fiji.plugin.Duplicate_Transformation
-Dynamic Reslice,fiji.stacks.Dynamic_Reslice
-Dynamic ROI Profiler,script:Analyze/Dynamic_ROI_Profiler.clj
-East,ij.plugin.filter.Shadows("east")
-Edit LUT As Text,script:Examples/Edit_LUT_As_Text.py
-Edit LUT...,ij.plugin.LUT_Editor
-Edit...,ij.plugin.Compiler("edit")
-Elastic Montaging,mpicbg.ij.plugin.ElasticMontage
-Elastic Stack Alignment,mpicbg.ij.plugin.ElasticAlign
-Embryos,ij.plugin.URLOpener("embryos.jpg")
-Enhance Contrast...,ij.plugin.ContrastEnhancer
-Enhance Local Contrast (CLAHE),mpicbg.ij.clahe.PlugIn
-Enlarge...,ij.plugin.RoiEnlarger
-EPS ...,sc.fiji.io.Export_EPS
-Erode,ij.plugin.filter.Binary("erode")
-Erode (3D),process3d.Erode_
-Exp,ij.plugin.filter.ImageMath("exp")
-Export Current Image as XML/HDF5,command:bdv.ij.ExportImagePlusPlugIn
-Export Current Image as XML/N5,command:bdv.ij.ExportImagePlusAsN5PlugIn
-Export Fused Sequence as XML/HDF5,command:bdv.ij.ExportSpimFusionPlugIn
-Export N5,command:org.janelia.saalfeldlab.n5.ij.N5Exporter
-Export Spim Sequence as XML/HDF5,command:bdv.ij.ExportSpimSequencePlugIn
-Extended Profile Plot,script:Examples/Extended_Profile_Plot.bsh
-Extract Images From PDF...,sc.fiji.io.Extract_Images_From_PDF
-Extract MOPS Correspondences,MOPS_ExtractPointRoi
-Extract SIFT Correspondences,SIFT_ExtractPointRoi
-extract stack under arealist,script:Examples/TrakEM2_Example_Scripts/extract_stack_under_arealist.py
-Fast FFT (2D/3D),registration3d.Fast_FourierTransform
-Fast VirtualStack Opener,QuickPALM.Run_MyMacro("Fast_VirtualStack_Opener.txt")
-FD Math...,ij.plugin.FFTMath
-FFT,ij.plugin.FFT("fft")
-FFT Options...,ij.plugin.FFT("options")
-FIB-SEM ...,sc.fiji.io.FIBSEM_Reader
-Fiji Cube,script:Examples/Fiji_Cube.ijm
-Fiji Logo 3D,script:Examples/Fiji_Logo_3D.js
-FilamentDetector,command:sc.fiji.filamentdetector.FilamentDetectorPlugin
-Fill Holes,ij.plugin.filter.Binary("fill")
-Fill ROI holes,Fill_holes
-Find Commands...,ij.plugin.CommandFinder
-Find Connected Regions,util.Find_Connected_Regions
-Find differences,FindIt_
-Find Dimension of Raw Image,script:Examples/Find_Dimension_of_Raw_Image.py
-Find Edges,ij.plugin.filter.Filters("edge")
-Find Jar For Class,script:Plugins/Utilities/Find_Jar_For_Class.bsh
-Find Maxima...,ij.plugin.filter.MaximumFinder
-Find Ops...,command:net.imagej.ui.swing.ops.FindOps
-Fire,ij.plugin.LutLoader("fire")
-First-instar brain (6.3MB),ij.plugin.URLOpener("http://samples.fiji.sc/first-instar-brain.zip")
-Fit Circle,ij.plugin.Selection("circle")
-Fit Circle to Image,fiji.util.Circle_Fitter
-Fit Ellipse,ij.plugin.Selection("ellipse")
-Fit Rectangle,ij.plugin.Selection("rect")
-Fit Spline,ij.plugin.Selection("spline")
-FITS...,ij.plugin.filter.Writer("fits")
-Fix Funny Filenames,script:File/Fix_Funny_Filenames.ijm
-Flip Horizontally,ij.plugin.filter.Transformer("fliph")
-Flip Vertically,ij.plugin.filter.Transformer("flipv")
-Flip Z,ij.plugin.StackReverser
-Flood Fill(3D),process3d.Flood_Fill
-FlowJ,FlowJ_
-Fluorescent Cells,ij.plugin.URLOpener("FluorescentCells.zip")
-Fly Brain,ij.plugin.URLOpener("flybrain.zip")
-Fonts...,ij.plugin.SimpleCommands("fonts")
-Fractal Box Count...,ij.plugin.filter.FractalBoxCounter
-Frangi Vesselness,command:net.imagej.ops.commands.filter.FrangiVesselness
-Fresh Start,ij.plugin.Options("fresh-start")
-From ROI Manager,ij.plugin.OverlayCommands("from")
-Fuse/Deconvolve Dataset,spim.fiji.plugin.Image_Fusion
-Gamma...,ij.plugin.filter.ImageMath("gamma")
-Gaussian Blur 3D...,ij.plugin.GaussianBlur3D
-Gaussian Blur...,ij.plugin.filter.GaussianBlur
-Gaussian Window MSE,mpicbg.ij.plugin.MSEGaussianFlow
-Gaussian-based stack focuser,sc.fiji.timelapse.Gaussian_Stack_Focuser
-Gel,ij.plugin.URLOpener("gel.gif")
-Gel Analyzer Options...,ij.plugin.GelAnalyzer("options")
-Geometry to Distance Map,sc.fiji.localThickness.EDT_S1D
-Gif...,ij.plugin.filter.Writer("gif")
-Gradient (3D),process3d.Gradient_
-Graph Cut,graphcut.Graph_Cut
-Gray Morphology,GrayMorphology_
-Gray Morphology...,GrayMorphology_("about")
-Grays,ij.plugin.LutLoader("grays")
-Green,ij.plugin.LutLoader("green")
-Grid...,ij.plugin.Grid
-Grid/Collection stitching,plugin.Stitching_Grid
-Grouped Z Project...,ij.plugin.GroupedZProjector
-HDF5 (append)...,sc.fiji.hdf5.HDF5_Writer_Vibez("append")
-HDF5 (new or replace)...,sc.fiji.hdf5.HDF5_Writer_Vibez("replace")
-HDF5...,sc.fiji.hdf5.HDF5_Reader_Vibez
-HeLa Cells (48-bit RGB),ij.plugin.URLOpener("hela-cells.zip")
-Helmholtz Analysis,Helmholtz_Analysis
-Help,ij.plugin.BrowserLauncher("https://docs.openmicroscopy.org/latest/bio-formats/users/index.html")
-Help on Menu Item,fiji.help.Context_Help
-Hide Overlay,ij.plugin.OverlayCommands("hide")
-Home,ij.plugin.SimpleCommands("showdirHome")
-Homogenize Ball Radius,script:Examples/TrakEM2_Example_Scripts/Homogenize_Ball_Radius.py
-HSB (32-bit),ij.plugin.Converter("HSB (32-bit)")
-HSB Stack,ij.plugin.Converter("HSB Stack")
-Hyperstack to Stack,ij.plugin.HyperStackConverter("hstostack")
-Hyperstack...,ij.plugin.HyperStackMaker
-Hypervolume Opener,sc.fiji.i5d.plugin.Hypervolume_Opener("")
-Ice,ij.plugin.LutLoader("ice")
-Icns ...,sc.fiji.io.Icns_Writer
-Icns...,sc.fiji.io.Icns_Reader
-ICO ...,sc.fiji.io.ICO_Writer
-ICO...,sc.fiji.io.ICO_Reader
-IFT (3D),process3d.IFT_
-IJ Robot,IJ_Robot
-Image,ij.plugin.SimpleCommands("showdirImage")
-Image Calculator...,ij.plugin.ImageCalculator
-Image Expression Parser,fiji.process.Image_Expression_Parser
-Image Expression Parser (Macro),fiji.process.Image_Expression_Parser("macro")
-Image Sequence...,ij.plugin.FolderOpener
-Image Sequence... ,ij.plugin.StackWriter
-Image to Results,ij.plugin.SimpleCommands("itor")
-Image to Selection...,ij.plugin.OverlayCommands("image-roi")
-Image To Tool Icon,script:Examples/Image_To_Tool_Icon.bsh
-Image with Overlay,ij.plugin.URLOpener("ImageWithOverlay.zip")
-Image... ,command:io.scif.commands.OpenDataset
-Image... ,command:io.scif.commands.SaveDataset
-Image5D Extensions,sc.fiji.i5d.plugin.Image5D_Extensions("")
-Image5D Stack to RGB,sc.fiji.i5d.plugin.Image5D_Stack_to_RGB("")
-Image5D to Stack,sc.fiji.i5d.plugin.Image5D_to_Stack("")
-Image5D...,sc.fiji.i5d.plugin.I5D_about("about")
-ImageJ,ij.plugin.SimpleCommands("showdirImageJ")
-ImageJ Properties,ij.plugin.JavaProperties
-ImageJ Website...,ij.plugin.BrowserLauncher
-ImageJ2...,command:net.imagej.legacy.ImageJ2Options
-Images to Stack,ij.plugin.ImagesToStack
-Implicit Interpolate Binary,Implicit_Interpolate_Binary
-In [+],ij.plugin.Zoom("in")
-Input/Output...,ij.plugin.Options("io")
-Insert Stack,video2.Insert_Stack
-Insert...,ij.plugin.StackInserter
-Inspect Java Objects,fiji.debugging.Object_Inspector
-Inspect Objects,command:org.scijava.ui.swing.commands.InspectObjects
-Install PlugIn...,sc.fiji.compat.PlugInInstaller
-Install...,ij.plugin.MacroInstaller
-Integral Block MSE,mpicbg.ij.plugin.MSEBlockFlow
-Integral Block PMCC,mpicbg.ij.plugin.PMCCBlockFlow
-Interactive Affine,Transform_Affine
-Interactive Moving Least Squares,Transform_MovingLeastSquaresMesh
-Interactive Perspective,Transform_Perspective
-Interactive Rigid,Transform_Rigid
-Interactive Similarity,Transform_Similarity
-Interactive Stack Rotation,Stack_Rotate
-Interactive Thin Plate Spline,Transform_ThinPlateSpline
-Interleave,Stack_Interleaver
-Internal Clipboard,ij.plugin.Clipboard("show")
-Interpolate,ij.plugin.Selection("interpolate")
-Inverse FFT,ij.plugin.FFT("inverse")
-Invert LUT,ij.plugin.LutLoader("invert")
-Invert LUTs,ij.plugin.SimpleCommands("invert")
-IPLab Reader...,sc.fiji.io.IPLab_Reader
-IsoData Classifier,IsoData_Classifier
-Janelia H265 Reader,org.janelia.it.fiji.plugins.h5j.H5j_Reader
-JavaScript,ij.plugin.NewPlugin("javascript")
-Jpeg...,ij.plugin.filter.Writer("jpeg")
-Kalman Stack Filter,Kalman_Filter
-Kappa - Curvature Analysis,command:sc.fiji.kappa.KappaPlugin
-Koala Binary...,sc.fiji.io.Koala_Bin_Reader
-Kuwahara Filter,Kuwahara_Filter
-KymographBuilder,command:sc.fiji.kymographBuilder.KymographBuilder
-Lab Stack,ij.plugin.Converter("Lab Stack")
-Label,ij.plugin.filter.Filler("label")
-Label Peaks,ij.plugin.GelAnalyzer("label")
-Label...,ij.plugin.filter.StackLabeler
-Labels...,ij.plugin.OverlayLabels
-Landmark Correspondences,Transform_Roi
-Laplace (3D),process3d.Laplace_
-Leaf,ij.plugin.URLOpener("leaf.jpg")
-Leica SP ...,leica.Leica_SP_Writer
-Leica SP...,leica.Leica_SP_Reader
-Lena (68K),ij.plugin.URLOpener("lena-std.tif")
-Level Sets,levelsets.ij.LevelSet
-Line Graph,ij.plugin.URLOpener("LineGraph.jpg")
-Line to Area,ij.plugin.Selection("toarea")
-Line Width...,ij.plugin.Options("line")
-Line Width... ,ij.plugin.frame.LineWidthAdjuster
-Linear Gradient,fiji.drawing.Linear_Gradient
-Linear Kuwahara,Kuwahara_LinearStructure_Filter_v3
-Linear Stack Alignment with SIFT,SIFT_Align
-list all threads,script:Examples/list_all_threads.py
-List Commands,ij.plugin.Hotkeys("list")
-List Elements,ij.plugin.OverlayCommands("list")
-List Shortcuts,ij.plugin.CommandLister("shortcuts")
-Load a TrackMate file,fiji.plugin.trackmate.LoadTrackMatePlugIn
-Load HDF5 File...,sc.fiji.hdf5.HDF5_Reader_Vibez
-Load Particles (.tif file - fast),QuickPALM.Load_particles_tableFromImg
-Local Thickness (complete process),sc.fiji.localThickness.Local_Thickness_Driver
-Log,ij.plugin.filter.ImageMath("log")
-LOI Interpolator,sc.fiji.timelapse.LOI_Interpolator
-LOI Interpolator Tool,sc.fiji.timelapse.LOI_Interpolator_Tool
-Look and Feel...,command:org.scijava.ui.swing.laf.OptionsLookAndFeel
-LSM...,LSM_Reader
-LSMReader...,LSM_Reader("about")
-LSMToolbox...,LSM_Toolbox("about")
-LSS16 ...,sc.fiji.io.LSS16_Writer
-LSS16...,sc.fiji.io.LSS16_Reader
-LUT...,ij.plugin.filter.Writer("lut")
-LUT... ,ij.plugin.LutLoader
-LUTs,ij.plugin.SimpleCommands("showdirLuts")
-M51 Galaxy (16-bits),ij.plugin.URLOpener("m51.zip")
-Macro,ij.plugin.NewPlugin("macro")
-Macro Functions...,ij.plugin.BrowserLauncher("https://wsr.imagej.net/developer/macro/functions.html")
-Macro Tool,ij.plugin.NewPlugin("macro-tool")
-Macro...,ij.plugin.filter.ImageMath("macro")
-Macro... ,ij.plugin.BatchProcessor
-Macros,ij.plugin.SimpleCommands("showdirMacros")
-Magenta,ij.plugin.LutLoader("magenta")
-Magic Montage Tools,ij.plugin.SimpleCommands("magic")
-Main Window [enter],ij.plugin.WindowOrganizer("imagej")
-Make Band...,ij.plugin.Selection("band")
-Make Binary,ij.plugin.Thresholder
-Make Circular Selection...,ij.plugin.CircularRoiMaker
-Make Composite,ij.plugin.CompositeConverter
-Make Fiji Package,fiji.packaging.Package_Maker
-Make Inverse,ij.plugin.Selection("inverse")
-Make Montage,sc.fiji.i5d.plugin.Make_Montage("")
-Make Montage...,ij.plugin.MontageMaker
-Make rectangular selection rounded,fiji.selection.Rounded_Rectangle
-Make Screencast,script:File/Make_Screencast.bsh
-Make Subset...,ij.plugin.SubstackMaker
-Make Substack...,ij.plugin.SubstackMaker
-Make Transition,video2.Make_Transition
-Malaria Sporozoites (9.2MB),ij.plugin.URLOpener("http://samples.fiji.sc/_malaria_parasites.tif")
-Mandelbrot Set,command:net.imagej.plugins.commands.debug.MandelbrotSetImage
-Manual landmark selection (3d),plugin.Manual_Landmark_Selection
-Manual Threshold...,script:Image/Adjust/Manual_Threshold....js
-Manual Tracking,Manual_Tracking
-Manual tracking with TrackMate,fiji.plugin.trackmate.ManualTrackingPlugIn
-Mask Of Nearby Points,util.Mask_Of_Nearby_Points
-Max (3D),process3d.Maximum_
-Max...,ij.plugin.filter.ImageMath("max")
-Maximize,ij.plugin.Zoom("max")
-Maximum (3D),process3d.Maximum_
-Maximum 3D...,ij.plugin.Filters3D("max")
-Maximum...,ij.plugin.filter.RankFilters("max")
-Mean,mpicbg.ij.plugin.Mean
-Mean 3D...,ij.plugin.Filters3D("mean")
-Mean...,ij.plugin.filter.RankFilters("mean")
-Measure AreaLists,script:Examples/TrakEM2_Example_Scripts/Measure_AreaLists.py
-Measure Connected Components,command:sc.fiji.labkit.ui.plugin.MeasureConnectedComponents
-Measure Overlay,ij.plugin.OverlayCommands("measure")
-Measure Stack...,ij.plugin.SimpleCommands("measure")
-Measure...,ij.plugin.BatchMeasure
-Median,ij.plugin.filter.Binary("median")
-Median (3D),process3d.Median_
-Median 3D...,ij.plugin.Filters3D("median")
-Median...,ij.plugin.filter.RankFilters("median")
-Memory & Threads...,sc.fiji.compat.Memory
-Merge Channels...,ij.plugin.RGBStackMerge
-Merge Cluster Jobs,spim.fiji.plugin.Merge_Cluster_Jobs
-MHD/MHA ...,sc.fiji.io.MetaImage_Writer
-MHD/MHA compressed ...,sc.fiji.io.MetaImage_CWriter
-MHD/MHA...,sc.fiji.io.MetaImage_Reader
-Min...,ij.plugin.filter.ImageMath("min")
-Minimum (3D),process3d.Minimum_
-Minimum 3D...,ij.plugin.Filters3D("min")
-Minimum...,ij.plugin.filter.RankFilters("min")
-Misc...,ij.plugin.Options("misc")
-Mitosis (5D stack),ij.plugin.URLOpener("Spindly-GFP.zip")
-Monitor Events...,ij.plugin.EventListener
-Monitor Memory...,ij.plugin.frame.MemoryMonitor
-Montage to Stack...,ij.plugin.StackMaker
-Move Roi,video2.Move_Roi
-Moving Least Squares,Moving_Least_Squares
-MRC Leginon ...,sc.fiji.io.Open_MRC_Leginon
-MRI Stack,ij.plugin.URLOpener("mri-stack.zip")
-MTrack2 ,MTrack2_
-Multi Kymograph,sc.fiji.multiKymograph.MultipleKymograph_
-Multi Overlay,sc.fiji.multiKymograph.MultipleOverlay_
-Multi-view deconvolution,fiji.plugin.Multi_View_Deconvolution
-Multi-view fusion,fiji.plugin.Multi_View_Fusion
-Multiple Image Processor,MultipleImageProcessor
-Multiply...,ij.plugin.filter.ImageMath("mul")
-Multithreaded Image Processing,script:Examples/Multithreaded_Image_Processing.clj
-N5,org.janelia.saalfeldlab.n5.ij.N5Importer
-N5 Viewer,org.janelia.saalfeldlab.n5.bdv.N5ViewerPlugin
-Name Landmarks and Register,landmarks.Name_Points
-NaN Background,ij.plugin.filter.ImageMath("nan")
-Neuron (5 channels),ij.plugin.URLOpener("Rat_Hippocampal_Neuron.zip")
-New Fiji News,fiji.Wiki_Editor("news")
-New Fiji Tutorial,fiji.Wiki_Editor("tutorial-maker")
-New Fiji Wiki Screenshot,fiji.Wiki_Editor("screenshot")
-New Hyperstack...,ij.plugin.HyperStackMaker
-New Image5D,sc.fiji.i5d.plugin.New_Image5D("")
-New Video,video2.New_Video
-Next Slice [>],ij.plugin.Animator("next")
-Nile Bend,ij.plugin.URLOpener("NileBend.jpg")
-Normalize Local Contrast,mpicbg.ij.plugin.NormalizeLocalContrast
-North,ij.plugin.filter.Shadows("north")
-Northeast,ij.plugin.filter.Shadows("northeast")
-Northwest,ij.plugin.filter.Shadows("northwest")
-Nrrd ...,sc.fiji.io.Nrrd_Reader
-Nrrd ... ,sc.fiji.io.Nrrd_Writer
-OME-TIFF...,loci.plugins.LociExporter("")
-Open,ij.plugin.filter.Binary("open")
-Open as Panel,ij.plugin.SimpleCommands("opencp")
-Open Current Image,command:bdv.ij.OpenImagePlusPlugIn
-Open Current Image With Labkit,command:sc.fiji.labkit.ui.plugin.LabkitPlugin
-Open Image File With Labkit,command:sc.fiji.labkit.ui.plugin.LabkitImportPlugin
-Open Image5D,sc.fiji.i5d.plugin.Open_Image5D("")
-Open Imaris (experimental),command:bdv.ij.OpenImarisPlugIn
-Open Series As Image5D,sc.fiji.i5d.plugin.Open_Series_As_Image5D("")
-Open Video,video2.Open_Video
-Open XML/HDF5,command:bdv.ij.BigDataViewerPlugIn
-Options...,ij.plugin.filter.Binary("options")
-OR...,ij.plugin.filter.ImageMath("or")
-Organ of Corti (4D stack),ij.plugin.URLOpener("organ-of-corti.zip")
-Out [-],ij.plugin.Zoom("out")
-Outline,ij.plugin.filter.Binary("outline")
-Page Setup...,ij.plugin.filter.Printer("setup")
-Pairwise stitching,plugin.Stitching_Pairwise
-Panorama equirectangular view,mpicbg.panorama.Panorama_View
-Particle Analyzer (3D),process3d.Particle_Analyzer_3D
-Particles,ij.plugin.URLOpener("particles.gif")
-Paste Control...,ij.plugin.frame.PasteController
-PDF ...,sc.fiji.io.PDF_Viewer
-PDF ... ,sc.fiji.io.PDF_Writer
-PGM...,ij.plugin.filter.Writer("pgm")
-Phase Map,sc.fiji.timelapse.Phase_Map
-PIV analysis,fiji.plugin.pivanalyser.PIV_analyser
-Plasma Cloud,script:Examples/Plasma_Cloud.rb
-Plot XY Profile,ij.plugin.StackPlotter
-Plot Z-axis Profile,ij.plugin.ZAxisProfiler
-Plots...,ij.plugin.Profiler("set")
-Plugin,ij.plugin.NewPlugin("plugin")
-Plugin Filter,ij.plugin.NewPlugin("filter")
-Plugin Frame,ij.plugin.NewPlugin("frame")
-Plugin Tool,ij.plugin.NewPlugin("plugin-tool")
-Plugins,ij.plugin.SimpleCommands("showdirPlugins")
-PNG...,ij.plugin.filter.Writer("png")
-Point Tool...,ij.plugin.PointToolOptions
-Points from Mask,fiji.selection.Binary_to_Point_Selection
-Prepare Cover Maker Database,script:Examples/CoverMaker/Prepare_Cover_Maker_Database.py
-Previous Slice [<],ij.plugin.Animator("previous")
-Proxy Settings...,ij.plugin.ProxySettings
-Put Behind [tab],ij.plugin.Commands("tab")
-Quantile Based Normalization,util.Quantile_Based_Normalization
-Quit,ij.plugin.Commands("quit")
-Radial Gradient,fiji.drawing.Radial_Gradient
-Radial Reslice,fiji.stacks.Radial_Reslice
-random noise example,script:Examples/random_noise_example.clj
-Raw Data...,ij.plugin.filter.Writer("raw")
-Raw...,ij.plugin.Raw
-Re-order Hyperstack ...,fiji.stacks.Hyperstack_rearranger
-Re-plot Lanes,ij.plugin.GelAnalyzer("replot")
-Read Reconstruct Project...,edu.utexas.clm.reconstructreader.reconstruct.Reconstruct_Reader
-Rebin (3D),process3d.Rebin_
-Reciprocal,ij.plugin.filter.ImageMath("reciprocal")
-Reconstruct Dataset,QuickPALM.Reconstruct_Dataset
-Record Desktop,script:Plugins/Utilities/Record_Desktop.py
-Record Window,script:Plugins/Utilities/Record_Window.py
-Record...,ij.plugin.frame.Recorder
-Red,ij.plugin.LutLoader("red")
-Red/Green,ij.plugin.LutLoader("redgreen")
-Redisplay Power Spectrum,ij.plugin.FFT("redisplay")
-Reduce Dimensionality...,ij.plugin.HyperStackReducer
-Reduce...,ij.plugin.StackReducer
-Refresh Menus,ij.plugin.ImageJ_Updater("menus")
-Register Virtual Stack Slices,register_virtual_stack.Register_Virtual_Stack_MT
-Release Notes...,ij.plugin.BrowserLauncher("https://wsr.imagej.net/notes.html")
-Remove Detections by Distance,spim.fiji.plugin.ThinOut_Detections
-Remove Detections Interactively,spim.fiji.plugin.Interactive_Remove_Detections
-Remove NaNs...,ij.plugin.filter.RankFilters("nan")
-Remove Outliers,mpicbg.ij.plugin.RemoveOutliers
-Remove Outliers...,ij.plugin.filter.RankFilters("outliers")
-Remove Overlay,ij.plugin.OverlayCommands("remove")
-Remove Shortcut...,ij.plugin.Hotkeys("remove")
-Remove Slice Labels,ij.plugin.SimpleCommands("remove")
-Remove Slope,Remove_Slope
-Rename...,ij.plugin.SimpleCommands("rename")
-Repeat a Recent Command,fiji.util.Recent_Commands
-Replace Red with Magenta,fiji.color.Convert_Red_To_Magenta
-Replace value,Replace_Value
-Report a Bug,Bug_Submitter.Bug_Submitter
-Resample,vib.Resample_
-Reset,ij.plugin.GelAnalyzer("reset")
-Reset...,ij.plugin.SimpleCommands("reset")
-Reset... ,ij.plugin.Options("reset")
-Reslice [/]...,ij.plugin.Slicer
-Reslice Z,Reslice_Z
-Results to Image,ij.plugin.SimpleCommands("rtoi")
-Results...,ij.plugin.MeasurementsWriter
-Results... ,ij.plugin.SimpleCommands("import")
-Retinex,Retinex_
-Reverse,ij.plugin.StackReverser
-RGB Color,ij.plugin.Converter("RGB Color")
-RGB Stack,ij.plugin.Converter("RGB Stack")
-RGB to CIELAB,RGB_to_CIELAB
-RGB to Image5D,sc.fiji.i5d.plugin.RGB_to_Image5D("")
-RGB to Luminance,util.RGB_to_Luminance
-Ridge Detection,de.biomedical_imaging.ij.steger.Lines_
-Rigid Registration,vib.RigidRegistration_
-ROF Denoise,fiji.denoise.ROF_Denoise
-Roi Defaults...,ij.gui.RoiDefaultsDialog
-ROI Manager...,ij.plugin.frame.RoiManager
-Rotate 90 Degrees Left,ij.plugin.filter.Transformer("left")
-Rotate 90 Degrees Right,ij.plugin.filter.Transformer("right")
-Rotate...,ij.plugin.Selection("rotate")
-Rotate... ,ij.plugin.filter.Rotator
-Rounded Rect Tool...,ij.plugin.RectToolOptions
-Run Script from File,command:org.scijava.batch.FileScriptBatchProcessor
-Run Script from Menu,command:org.scijava.batch.MenuScriptBatchProcessor
-Run...,ij.plugin.Macro_Runner
-Salt and Pepper,ij.plugin.filter.SaltAndPepper
-Same Slice in Multiple Images,script:Examples/Same_Slice_in_Multiple_Images.rb
-Sample Variance,mpicbg.ij.plugin.SampleVariance
-Save Image5D,sc.fiji.i5d.plugin.Save_Image5D("")
-Save Particles (.tif file - fast),QuickPALM.Save_particles_table2img
-Save to HDF5 File (append)...,sc.fiji.hdf5.HDF5_Writer_Vibez("append")
-Save XY Coordinates...,ij.plugin.XYCoordinates
-Scale Bar...,ij.plugin.ScaleBar
-Scale to DPI,script:Image/Adjust/Scale_to_DPI.js
-Scale to Fit,ij.plugin.Zoom("scale")
-Scale... ,ij.plugin.RoiScaler
-Script Interpreter,command:org.scijava.ui.swing.script.ScriptInterpreterPlugin
-Script...,command:org.scijava.ui.swing.script.ScriptEditor
-Scriptable load HDF5...,sc.fiji.hdf5.HDF5_Simple_Reader
-Scriptable save HDF5 (append)...,sc.fiji.hdf5.HDF5_Simple_Writer("append")
-Seam remover,Seam_Remover
-Search Bar...,command:net.imagej.legacy.search.SearchOptions
-Search...,ij.plugin.SimpleCommands("search")
-Segment blob in 3D Viewer,ij3d.segmentation.Blob_Segmentation_in_3D
-Segment Image With Labkit,command:sc.fiji.labkit.ui.plugin.SegmentImageWithLabkitPlugin
-Segmentation Editor,Segmentation_Editor
-Select Bounding Box,fiji.selection.Select_Bounding_Box
-Selection...,ij.plugin.filter.RoiWriter
-Series Labeler,Series_Labeler
-Set Active Axis...,command:net.imagej.plugins.commands.axispos.SetActiveAxis
-Set Channel Display,sc.fiji.i5d.plugin.Set_Channel_Display("")
-Set Channel Labels,sc.fiji.i5d.plugin.Set_Channel_Labels("")
-Set Color By Wavelength,script:Image/Color/Set_Color_By_Wavelength.ijm
-Set Label...,ij.plugin.SimpleCommands("set")
-Set Measurements...,ij.plugin.filter.Analyzer("set")
-Set Position,sc.fiji.i5d.plugin.Set_Position("")
-Set Scale...,ij.plugin.filter.ScaleDialog
-Set Slice...,ij.plugin.Animator("set")
-Set...,ij.plugin.filter.ImageMath("set")
-Set... ,ij.plugin.Zoom("set")
-Shadows Demo,ij.plugin.filter.Shadows("demo")
-Shape Index Map,fiji.geom.Shape_Index_Map
-Shape-based averaging,Rohlfing_SBA
-Sharpen,ij.plugin.filter.Filters("sharpen")
-Show Amira Surface,isosurface.AmiraSurface
-Show Circular Masks...,ij.plugin.filter.RankFilters("masks")
-Show Color Surfaces,isosurface.Show_Colour_Surfaces
-Show label centers,Show_Label_Centers
-Show LSMToolbox,LSM_Toolbox("")
-Show LUT,ij.plugin.filter.LutViewer
-Show Overlay,ij.plugin.OverlayCommands("show")
-Simulate Color Blindness,Daltonize_
-Sintered Alumina (2.6MB),ij.plugin.URLOpener("http://fiji.sc/samples/Sintered_Alumina.tif.zip")
-Size...,ij.plugin.Resizer
-Skeletonize,ij.plugin.filter.Binary("skel")
-Skeletonize (2D/3D),sc.fiji.skeletonize3D.Skeletonize3D_
-Slice Keeper,Slice_Keeper
-Slice Remover,Slice_Remover
-Smooth (3D),process3d.Smooth_
-South,ij.plugin.filter.Shadows("south")
-Southeast,ij.plugin.filter.Shadows("southeast")
-Southwest,ij.plugin.filter.Shadows("southwest")
-Specify Calibration,spim.fiji.plugin.Specify_Calibration
-Specify...,ij.plugin.SpecifyROI
-Spectrum,ij.plugin.LutLoader("spectrum")
-Spheres and Tubes in 3D,customnode.Mesh_Maker
-SPIM,spimopener.SPIM_Opener
-Spirals ,script:File/Open_Samples/Spirals_.ijm
-Spline Deformation Generator,SplineDeformationGenerator.SplineDeformationGenerator_
-Split Channels,ij.plugin.ChannelSplitter
-Square,ij.plugin.filter.ImageMath("sqr")
-Square Root,ij.plugin.filter.ImageMath("sqrt")
-Stack Difference,sc.fiji.multiKymograph.StackDifference_
-Stack From List...,ij.plugin.ListVirtualStack
-Stack Slicer,loci.plugins.Slicer("")
-Stack Sorter,Stack_Sorter
-Stack Splitter,Stack_Splitter
-Stack to Hyperstack...,ij.plugin.HyperStackConverter("stacktohs")
-Stack to Image5D,sc.fiji.i5d.plugin.Stack_to_Image5D("")
-Stack to Images,ij.plugin.StackEditor("toimages")
-Stack to RGB,ij.plugin.RGBStackConverter
-Standard Deviation,mpicbg.ij.plugin.StandardDeviation
-Start Animation [\],ij.plugin.Animator("start")
-Start Cluster...,edu.utexas.clm.archipelago.Fiji_Archipelago("gui")
-start viewer,view5d.View5D_("")
-Startup Macros...,ij.plugin.Commands("startup")
-Startup...,ij.plugin.Startup
-Statistical Region Merging,SRM_
-Statistics,ij.plugin.Stack_Statistics
-Stitch Collection of Images,Stitch_Image_Collection
-Stitch Grid of Images,Stitch_Image_Grid
-Stitch Sequence of Grids of Images,Stitch_Image_Grid_Sequence
-Stop Animation,ij.plugin.Animator("stop")
-Straight Lines,script:File/Open_Samples/Straight_Lines.ijm
-Straighten...,ij.plugin.Straightener
-Stress Test,edu.utexas.clm.archipelago.example.Stress_Test("")
-Striped Circles,script:File/Open_Samples/Striped_Circles.ijm
-Subtract Background...,ij.plugin.filter.BackgroundSubtracter
-Subtract...,ij.plugin.filter.ImageMath("sub")
-Summarize,ij.plugin.filter.Analyzer("sum")
-Surface Plot...,ij.plugin.SurfacePlotter
-SurfaceJ,SurfaceJ_
-Surfaceness,features.Surfaceness_
-SVG...,sc.fiji.io.SVG_Reader
-Swap Quadrants,ij.plugin.FFT("swap")
-Sync Measure 3D,Sync_Measure_3D("")
-Sync Measure 3D...,Sync_Measure_3D("about")
-Sync Windows,Sync_Windows("")
-Sync Windows...,Sync_Windows("about")
-Synchronize Windows,ij.plugin.frame.SyncWindows
-System Information,command:org.scijava.plugins.commands.debug.SystemInformation
-T1 Head (16-bits),ij.plugin.URLOpener("t1-head.zip")
-T1 Head Renderings,ij.plugin.URLOpener("t1-rendering.zip")
-T2 Select All,script:Examples/TrakEM2_Example_Scripts/T2_Select_All.py
-T2 set all transforms to identity,script:Examples/TrakEM2_Example_Scripts/T2_set_all_transforms_to_identity.py
-Table... ,ij.plugin.SimpleCommands("table")
-Table... ,command:org.scijava.table.io.ExportTableCommand
-Task Monitor Bar...,command:net.imagej.legacy.task.TaskMonitorOptions
-TEM Filter,ij.plugin.URLOpener("TEM_filter_sample.jpg")
-temp,ij.plugin.SimpleCommands("showdirTemp")
-Temporal-Color Code,script:Image/Hyperstacks/Temporal-Color_Code.ijm
-Test Block Matching Parameters,mpicbg.ij.plugin.BlockMatching_TestParameters
-Test Cluster,edu.utexas.clm.archipelago.example.Test_Cluster("")
-Test Java3D,Test_Java3D
-Test Marching Cubes,MC_Test
-Text File... ,ij.plugin.TextFileReader
-Text Image...,ij.plugin.filter.Writer("text")
-Text Image... ,ij.plugin.TextReader
-Text Window...,ij.plugin.NewPlugin("text+dialog")
-Text...,ij.plugin.TextWriter
-The Hue Game,script:Examples/The_Hue_Game.bsh
-Thread killer,Thread_Killer
-Threads,ij.plugin.ThreadLister
-TIFF Virtual Stack...,ij.plugin.FileInfoVirtualStack
-Tiff...,ij.plugin.filter.Writer("tiff")
-Tile,ij.plugin.WindowOrganizer("tile")
-Time Stamper,Time_Stamper
-To Bounding Box,ij.plugin.Selection("tobox")
-To ROI Manager,ij.plugin.OverlayCommands("to")
-To Selection,ij.plugin.Zoom("to")
-ToAST,ToAST25_
-Toggle Cluster Processing,spim.fiji.plugin.Toggle_Cluster_Options
-Toggle Overlay,ij.plugin.OverlayCommands("toggle")
-Top Hat...,ij.plugin.filter.RankFilters("tophat")
-TorstenRaw GZ Reader...,sc.fiji.io.TorstenRaw_GZ_Reader
-TrackMate,fiji.plugin.trackmate.TrackMateRunner
-Tracks for TrackMate (807K),ij.plugin.URLOpener("http://fiji.sc/samples/FakeTracks.tif")
-Trainable Segmentation,trainableSegmentation.Trainable_Segmentation
-Trainable Segmentation 2D,edu.utexas.archipelago.plugin.Batch_Weka_Segmentation
-Trainable Weka Segmentation,trainableSegmentation.Weka_Segmentation
-Trainable Weka Segmentation 3D,trainableSegmentation.Weka_Segmentation("3D")
-TrakEM2 (blank),ini.trakem2.New_Project("blank")
-TrakEM2 (from template),ini.trakem2.New_Project
-TrakEM2 Folder Watcher,fsalign.FS_Align_TrakEM2
-TrakEM2 XML...,ini.trakem2.Open_Project
-Transfer Channel Settings,sc.fiji.i5d.plugin.Transfer_Channel_Settings("")
-Transform Virtual Stack Slices,register_virtual_stack.Transform_Virtual_Stack_MT
-Translate...,ij.plugin.filter.Translator
-Translate... ,ij.plugin.Selection("translate")
-Tree Rings,ij.plugin.URLOpener("Tree_Rings.jpg")
-Triangle Algorithm,Triangle_Algorithm
-Tubeness,features.Tubeness_
-Ultimate Points,ij.plugin.filter.EDM("points")
-Unsharp Mask...,ij.plugin.filter.UnsharpMask
-Update Bio-Formats Plugins,loci.plugins.Updater("")
-Update ImageJ...,ij.plugin.ImageJ_Updater
-Update QuickPALM,QuickPALM.Run_MyMacro("Update_.txt")
-Update...,command:net.imagej.ui.swing.updater.ImageJUpdater
-Upload Image to Fiji Wiki,fiji.Upload_Image_To_Wiki
-Upload Sample Image...,command:net.imagej.plugins.commands.upload.SampleImageUploader
-URL...,ij.plugin.URLOpener
-V3Draw...,Vaa3d_Writer
-Vaa3d...,org.janelia.vaa3d.reader.Vaa3d_Reader
-Variance 3D...,ij.plugin.Filters3D("var")
-Variance...,ij.plugin.filter.RankFilters("variance")
-VIB Protocol,VIB_Protocol
-Vibez validate...,sc.fiji.hdf5.Vibez_Validate
-View5D ,view5d.View5D_
-Virtual Image5D Opener,sc.fiji.i5d.plugin.Virtual_Image5D_Opener("")
-Virtual Stack...,ij.plugin.BatchProcessor("stack")
-Visual grep,Visual_Grep
-Visualize Detections,spim.fiji.plugin.Visualize_Detections
-Visualize OME Metadata,command:sc.fiji.omevisual.OMEVisual
-Volume Calculator,volumeCalculator.Volume_Calculator
-Volume Reconstructor,Volume_Reconstructor_
-Volume Viewer,fiji.plugin.volumeviewer.Volume_Viewer
-VolumeJ,VolumeJ_
-Voronoi,ij.plugin.filter.EDM("voronoi")
-Walking Average,sc.fiji.multiKymograph.WalkingAverage_
-Wand Tool...,ij.plugin.WandToolOptions
-Watch Events,command:org.scijava.ui.swing.commands.WatchEvents
-Watershed,ij.plugin.filter.EDM("watershed")
-Wavefront .OBJ ...,marchingcubes.ExportMesh_
-West,ij.plugin.filter.Shadows("west")
-Window/Level...,ij.plugin.frame.ContrastAdjuster("wl")
-Write Reconstruct Project...,edu.utexas.clm.reconstructreader.trakem2.Reconstruct_Writer
-XOR...,ij.plugin.filter.ImageMath("xor")
-XPM ...,sc.fiji.io.XPM_Writer
-XY Coordinates...,ij.plugin.filter.XYWriter
-XY Coordinates... ,ij.plugin.XY_Reader
-Yellow,ij.plugin.LutLoader("yellow")
-Z Project,sc.fiji.i5d.plugin.Z_Project("")
-Z Project...,ij.plugin.ZProjector
-Z-Spacing Correction,org.janelia.thickness.plugin.ZPositionCorrection
-ZIP...,ij.plugin.filter.Writer("zip")
diff --git a/macro-functions.txt b/macro-functions.txt
deleted file mode 100644
index ee57405..0000000
--- a/macro-functions.txt
+++ /dev/null
@@ -1,807 +0,0 @@
-#ImageJ Macro Commands File Generated from https://imagej.net/ij/developer/macro/functions.html Last updated 2023/12/15.
-abs(n) Returns the absolute value of n.
-acos(n) Returns the inverse cosine (in radians) of n.
-Array These functions operate on arrays. Refer to the ArrayFunctions macro for examples.
-Array.concat(array1, array2)Returns a new array created by joining two or more arrays or values.
-Array.copy(array)Returns a copy of array.
-Array.deleteValue(array, value)Returns a version of array where all numeric or string elements in the array that contain value have been deleted .
-Array.deleteIndex(array, index)Returns a version of array where the element with the specified index has been deleted.
-Array.fill(array, value)Assigns the specified numeric value to each element of array.
-Array.filter(array, filter) Returns an array containing the elements of 'array' that contain 'filter', where 'array' is an array of strings. Enclose the filter in parans to do regular expression matching. Requires 1.53f.
-Array.findMaxima(array, tolerance)Returns an array holding the peak positions (sorted with descending strength). 'Tolerance' is the minimum amplitude difference needed to separate two peaks. With v1.51n and later, there is an optional 'edgeMode' argument: 0=include edges, 1=exclude edges(default), 2=circular array. Examples.
-Array.findMinima(array, tolerance)Returns an array holding the minima positions.
-Array.fourier(array, windowType)Calculates and returns the Fourier amplitudes of array. WindowType can be "none", "Hamming", "Hann", or "flat-top", or may be omitted (meaning "none"). See the TestArrayFourier macro for an example and more documentation.
-Array.getSequence(n)Returns an array containing the numeric sequence 0,1,2...n-1.
-Array.getStatistics(array, min, max, mean, stdDev)Returns the min, max, mean, and stdDev of array, which must contain all numbers.
-Array.print(array)Prints the array on a single line.
-Array.rankPositions(array)Returns, as an array, the rank position indexes of array, starting with the index of the smallest value.
-Array.resample(array, len)Returns an array which is linearly resampled to a different length.
-Array.reverse(array)Reverses (inverts) the order of the elements in array.
-Array.show(array)Displays the contents of array in a window.
-Array.show("title", array1, array2, ...)Displays one or more arrays in a Results window. If title (optional) is "Results", the window will be the active Results window, otherwise, it will be a dormant Results window (see also IJ.renameResults). If title ends with "(indexes)", a 0-based Index column is shown. If title ends with "(row numbers)", the row number column is shown.
-Array.slice(array, start, end)Extracts a part of an array and returns it.
-Array.sort(array)Sorts array, which must contain all numbers or all strings. String sorts are case-insensitive.
-Array.sort(array1, array2, array3...)Sorts multiple arrays, where all the arrays adopt the sort order of array1.
-Array.trim(array, n)Returns an array that contains the first n elements of array.
-Array.rotate(array, d)Rotates the array elements by 'd' steps (positive 'd' = rotate right). Requires 1.51n. Examples.
-Array.getVertexAngles(xArr, yArr, arm)From a closed contour given by 'xArr', 'yArr', an array is returned holding vertex angles in degrees (straight=0, convex = positive if contour is clockwise). Set 'arm'=1 to calculate the angle from the closest vertex points left and right, or use arm>1 for more distant neighbours and smoother results. Requires 1.51n. Examples.
-asin(n) Returns the inverse sine (in radians) of n.
-atan(n) Calculates the inverse tangent (arctangent) of n. Returns a value in the range -PI/2 through PI/2.
-atan2(y, x) Calculates the inverse tangent of y/x and returns an angle in the range -PI to PI, using the signs of the arguments to determine the quadrant. Multiply the result by 180/PI to convert to degrees.
-autoUpdate(boolean) If boolean is true, the display is refreshed each time lineTo(), drawLine(), drawString(), etc. are called, otherwise, the display is refreshed only when updateDisplay() is called or when the macro terminates.
-beep() Emits an audible beep.
-bitDepth() Returns the bit depth of the active image: 8, 16, 24 (RGB) or 32 (float).
-calibrate(value) Uses the calibration function of the active image to convert a raw pixel value to a density calibrated value. The argument must be an integer in the range 0-255 (for 8-bit images) or 0-65535 (for 16-bit images). Returns the same value if the active image does not have a calibration function.
-call("class.method", arg1, arg2, ...) Calls a public static method in a Java class, passing an arbitrary number of string arguments, and returning a string. Refer to the CallJavaDemo macro and the ImpProps plugin for examples.
-call("class.method") Calls a public static no-argument method in a Java class and returns a string.
-changeValues(v1, v2, v3) Changes pixels in the image or selection that have a value in the range v1-v2 to v3. For example, changeValues(0, 5, 5) changes all pixels less than 5 to 5, and changeValues(0x0000ff, 0x0000ff, 0xff0000) changes all blue pixels in an RGB image to red. In ImageJ 1.52d or later, use changeValues(NaN, NaN, value) to replaces NaN values.
-charCodeAt(string, index) Returns the Unicode value of the character at the specified index in string. Index values can range from 0 to lengthOf(string). Use the fromCharCode() function to convert one or more Unicode characters to a string.
-close() Closes the active image. This function has the advantage of not closing the "Log" or "Results" window when you meant to close the active image. Use run("Close") to close non-image windows.
-close(pattern) Closes windows whose title matches 'pattern', which can contain the wildcard characters '*' (matches any character sequence) and '?' (matches single character). For example, close("Histo*") could be used to dispose all histogram windows. Non-image windows like "Roi Manager" have to be specified without wildcards. For text windows, wildcards are allowed if 'pattern' ends with ".txt", ".ijm", ".js" etc. Use close("*") to close all image windows. Use close(pattern, "keep") to not close text or image windows with changes. If 'pattern' is "\\Others", all images except the front image are closed. The most recent macro window is never closed.
-close("*") Closes all image windows.
-close("\\Others") Closes all images except for the front image.
-Color Functions for working with colors, available in ImageJ 1.53h and later.
-Color.set(string) Sets the drawing color, where 'string' is "red", "blue", etc., or a hex value like "#ff0000".
-Color.set(value) Sets the drawing color. For 8 bit images, 0<=value<=255. For 16 bit images, 0<=value<=65535. With RGB images, use hex constants (e.g., 0xff0000 for red).
-Color.setForeground(string) Sets the foreground color, where 'string' is "red", "blue", etc., or a hex value like "#ff0000".
-Color.setForegroundValue(value) Sets the foreground color to grayscale, where 'value' is a number between 0 and 255.
-Color.setBackground(string) Sets the background color, where 'string' is "red", "blue", etc., or a hex value like "#ff0000".
-Color.setBackgroundValue(value) Sets the background color to grayscale, where 'value' is a number between 0 (black) and 255 (white).
-Color.setForeground(r, g, b) Sets the foreground color, where r, g, and b are >= 0 and <= 255.
-Color.setBackground(r, g, b) Sets the background color, where r, g, and b are >= 0 and <= 255.
-Color.foreground Returns the foreground color as a string, for example "red" or "#ff0000".
-Color.background Returns the background color as a string, for example "cyan" or "#00ffff".
-Color.toString(r, g, b)Converts an r,g,b color to a string.
-Color.toArray(string)Converts a color (e.g., "red" or "#ff0000") to a three element array.
-Color.getLut(reds, greens, blues)Returns three arrays containing the red, green and blue intensity values from the current lookup table. See the LookupTables macros for examples.
-Color.setLut(reds, greens, blues)Creates a new lookup table and assigns it to the current image. Three input arrays are required, each containing 256 intensity values.
-Color.wavelengthToColor(wavelength)Converts a wavelength (380-750 nm) into a color in string format (e.g., "#0031ff"). See also: Help>Examples>Plots>Plot With Spectrum.
-cos(angle)Returns the cosine of an angle (in radians).
-d2s(n, decimalPlaces)Converts the number n into a string using the specified number of decimal places. Uses scientific notation if 'decimalPlaces is negative. Note that d2s stands for "double to string".
-debug(arg)Calls the macro debugger, where 'arg' is "break" (the default), "run", "trace", "fast-trace", "dump" or "throw". Call debug("dump") to display the contents of the symbol table, the tokenized macro code and the variable stack. Call debug("throw") to display an example "Exception" window.
-Dialog.create("Title")Creates a modal dialog box with the specified title, or use Dialog.createNonBlocking("Title") to create a non-modal dialog. Call Dialog.addString(), Dialog.addNumber(), etc. to add components to the dialog. Call Dialog.show() to display the dialog and Dialog.getString(), Dialog.getNumber(), etc. to retrieve the values entered by the user. Refer to the DialogDemo macro for an example.
-Dialog.createNonBlocking("Title")Creates a non-modal dialog box with the specified title.
-Dialog.addMessage(string)Adds a message to the dialog. The message can be broken into multiple lines by inserting new line characters ("\n") into the string.
-Dialog.addMessage(string, fontSize, fontColor)Adds a message to the dialog using a specified font size and color (example). The message can be broken into multiple lines by inserting new line characters ("\n") into the string. The 'fontSize' and 'fontColor' arguments are optional.
-Dialog.addString(label, initialText)Adds a text field to the dialog, using the specified label and initial text.
-Dialog.addString(label, initialText, columns)Adds a text field to the dialog, where columns specifies the field width in characters.
-Dialog.addNumber(label, default)Adds a numeric field to the dialog, using the specified label and default value.
-Dialog.addNumber(label, default, decimalPlaces, columns, units)Adds a numeric field, using the specified label and default value. DecimalPlaces specifies the number of digits to right of decimal point, columns specifies the the field width in characters and units is a string that is displayed to the right of the field.
-Dialog.addSlider(label, min, max, default)Adds a slider controlled numeric field to the dialog, using the specified label, and min, max and default values (example). Values with decimal points are used when (max-min)<=5 and min, max or default are non-integer.
-Dialog.addCheckbox(label, default)Adds a checkbox to the dialog, using the specified label and default state (true or false).
-Dialog.addCheckboxGroup(rows, columns, labels, defaults)Adds a rowsxcolumns grid of checkboxes to the dialog, using the specified labels and default states (example).
-Dialog.addRadioButtonGroup(label, items, rows, columns, default)Adds a group of radio buttons to the dialog, where 'label' is the group label, 'items' is an array containing the button labels, 'rows' and 'columns' specify the grid size, and 'default' is the label of the default button. (example).
-Dialog.addChoice(label, items)Adds a popup menu to the dialog, where items is a string array containing the menu items.
-Dialog.addChoice(label, items, default)Adds a popup menu, where items is a string array containing the choices and default is the default choice.
-Dialog.addDirectory(label, defaultPath)Adds a directory field and "Browse" button. The field width is determined by the length of 'defaultPath', with a minimum of 25 columns. Use Dialog getString to retrieve the directory path. Use File.setDefaultDir() to set the default directory used when the user clicks on "Browse". Requires 1.53d.
-Dialog.addFile(label, defaultPath)Adds a file field and "Browse" button. The field width is determined by the length of 'defaultPath', with a minimum of 25 columns. Use Dialog getString to retrieve the file path. Requires 1.53d.
-Dialog.addImage(pathOrURL)Adds an image to the dialog. The 'pathOrURL' argument can be a file path (e.g., "/Users/wayne/Downloads/blobs.tif") or a URL (e.g., "https://imagej.net/images/blobs.gif").
-Dialog.addImageChoice(label)Adds a popup menu that lists the currently open images. Use Dialog getImageChoice() to retrieve the title of the selected image. The macro aborts if there are no open images. Requires 1.53d.
-Dialog.addImageChoice(label, defaultImage)This a version of addImageChoice() with a second argument for specifying the selected image in the dropdown menu. Requires 1.53s.
-Dialog.addHelp(url)Adds a "Help" button that opens the specified URL in the default browser. This can be used to supply a help page for this dialog or macro. With v1.46b or later, displays an HTML formatted message if 'url' starts with "" (example).
-Dialog.addToSameRow()Makes the next item added appear on the same row as the previous item. May be used for addNumericField, addSlider, addChoice, addCheckbox, addString, addMessage, and before the showDialog() method. In the latter case, the buttons appear to the right of the previous item. Note that addMessage (and addString if a width of more than 8 is specified) use the remaining width, so it must be the last item of a row. Requires 1.51r.
-Dialog.setInsets(top, left, bottom)Overrides the default insets (margins) used for the next component added to the dialog.
-addMessage: 0,20,0 (empty string) or 10,20,0
-addCheckbox: 15,20,0 (first checkbox) or 0,20,0
-addCheckboxGroup: 10,0,0
-addNumericField: 5,0,3 (first field) or 0,0,3
-addStringField: 5,0,5 (first field) or 0,0,5
-addChoice: 5,0,5 (first field) or 0,0,5
-Dialog.setLocation(x, y)Sets the screen location where this dialog will be displayed.
-Dialog.getLocation(x, y)Returns the screen location of this dialog. Requires 1.54g.
-Dialog.enableYesNoCancel(yesLabel,noLabel)Make this a Yes/No/Cancel dialog with custom labels. Requires 1.54h. (example).
-Dialog.getYesNoCancelReturns "yes" if the users clicks on the "Yes" button in a Yes/No/Cancel dialog and "no" if the user clicks on "No". The macro is aborted if the user clicks on "Cancel". Requires 1.54h.
-Dialog.show()Displays the dialog and waits until the user clicks "OK" or "Cancel". The macro terminates if the user clicks "Cancel".
-Dialog.getString()Returns a string containing the contents of the next text, directory or file field.
-Dialog.getNumber()Returns the contents of the next numeric field.
-Dialog.getCheckbox()Returns the state (true or false) of the next checkbox.
-Dialog.getChoice()Returns the selected item (a string) from the next popup menu.
-Dialog.getRadioButton()Returns the selected item (a string) from the next radio button group.
-Dialog.getImageChoice()Returns the title of the image selected in the next image choice popup menu.
-doCommand("Command")Runs an ImageJ menu command in a separate thread and returns immediately. As an example, doCommand("Start Animation") starts animating the current stack in a separate thread and the macro continues to execute. Use run("Start Animation") and the macro hangs until the user stops the animation.
-doWand(x, y)Equivalent to clicking on the current image at (x, y) with the wand tool. Note that some objects, especially one pixel wide lines, may not be reliably traced unless they have been thresholded (highlighted in red) using setThreshold.
-doWand(x, y, tolerance, mode)Traces the boundary of the area with pixel values within 'tolerance' of the value of the pixel at (x, y). 'mode' can be "4-connected", "8-connected" or "Legacy". "Legacy" is for compatibility with previous versions of ImageJ; it is ignored if 'tolerance' > 0. If 'mode' contains 'smooth', the contour is smoothed by interpolation (example).
-drawLine(x1, y1, x2, y2)Draws a line between (x1, y1) and (x2, y2). Use setColor() to specify the color of the line and setLineWidth() to vary the line width. See also: Overlay.drawLine.
-drawOval(x, y, width, height)Draws the outline of an oval using the current color and line width. See also: fillOval, setColor, setLineWidth, autoUpdate and Overlay.drawEllipse.
-drawRect(x, y, width, height)Draws the outline of a rectangle using the current color and line width. See also: fillRect, setColor, setLineWidth, autoUpdate and Overlay.drawRect
-drawString("text", x, y)Draws text at the specified location. The first character is drawn obove and to the right of (x, y). Call setFont() to specify the font. Call setJustification() to have the text centered or right justified. Call getStringWidth() to get the width of the text in pixels. Refer to the TextDemo macro for examples and to DrawTextWithBackground to see how to draw text with a background.
-drawString("text", x, y, background)Draws text at the specified location with a filled background (examples).
-dump()Writes the contents of the symbol table, the tokenized macro code and the variable stack to the "Log" window.
-endsWith(string, suffix)Returns true (1) if string ends with suffix. See also: startsWith, indexOf, substring, matches.
-eval(macro)Evaluates (runs) one or more lines of macro code. An optional second argument can be used to pass a string to the macro being evaluated. See also: EvalDemo macro and runMacro function.
-eval("script", javascript)Evaluates the JavaScript code contained in the string javascript and returns, as a string, the value of the last statement executed. For example eval("script", "IJ.getInstance().setAlwaysOnTop(true);"). See also: runMacro(path, arg).
-eval("js", script)Evaluates the JavaScript code contained in the string script and returns, as a string, the value of the last statement executed. For example eval("js", "Prefs.blackBackground") returns either "true" or "false".
-eval("bsh", script)Evaluates the BeanShell code contained in the string script.
-eval("python", script)Evaluates the Python code contained in the string script.
-exec(string or strings)Executes a native command and returns the output of that command as a string. Also opens Web pages in the default browser and documents in other applications (e.g., Excel). With commands with multiple arguments, each argument should be passed as a separate string. For example exec("open", "/Users/wayne/test.jpg", "-a", "/Applications/Gimp.app"); Refer to the ExecExamples macro for examples.
-exit Terminates execution of the macro.
-exit("error message")Terminates execution of the macro and displays an error message.
-exp(n)Returns the exponential number e (i.e., 2.718...) raised to the power of n.
-Ext These are functions that have been added to the macro language by plugins using the MacroExtension interface. The Image5D_Extensions plugin, for example, adds functions that work with Image5D. The Serial Macro Extensions plugin adds functions, such as Ext.open("COM8", 9600, "") and Ext.write("a"), that talk to serial devices.
-File These functions allow you to get information about a file, read or write a text file, create a directory, or to delete, rename or move a file or directory. Note that these functions return a string, with the exception of File.length, File.exists, File.isDirectory, File.rename and File.delete when used in an assignment statement, for example "length=File.length(path)". The FileDemo macro demonstrates how to use these functions. See also: getDirectory and getFileList.
-File.append(string, path)Appends string to the end of the specified file.
-File.close(f)Closes the specified file, which must have been opened using File.open().
-File.copy(path1, path2)Copies a file.
-File.dateLastModified(path)Returns the date and time the specified file was last modified.
-File.delete(path)Deletes the specified file or directory. With v1.41e or later, returns "1" (true) if the file or directory was successfully deleted. If the file is a directory, it must be empty. The file must be in the user's home directory, the ImageJ directory or the temp directory.
-File.directoryThe directory path of the last file opened using a file open dialog, a file save dialog, drag and drop, open(path) or runMacro(path).
-File.exists(path)Returns "1" (true) if the specified file exists.
-File.getName(path)Returns the file name (e.g., "blobs.tif") from path.
-File.getNameWithoutExtension(path)Returns the name (e.g., "blobs") from path without the extension.
-File.getDirectory(path)Returns the directory (e.g., "C:/Users/wayne/images/") from path.
-File.getDefaultDirReturns the default directory used by file open dialogs or the current working directory if called from a command line macro and File.setDefaultDir() has not been called.
-File.setDefaultDir(directoryPath)Sets the default directory used by file open dialogs.
-File.getParent(path)Returns the parent of the file specified by path.
-File.isFile(path)Returns "1" (true) if the specified file is not a directory.
-File.isDirectory(path)Returns "1" (true) if the specified file is a directory.
-File.lastModified(path)Returns the time the specified file was last modified as the number of milliseconds since January 1, 1970.
-File.length(path)Returns the length in bytes of the specified file as a string, or as a number when used in an assignment statement, for example "length=File.length(path)".
-File.makeDirectory(path)Creates a directory.
-File.nameThe name of the last file opened using a file open dialog, a file save dialog, drag and drop, or the open(path) function.
-File.nameWithoutExtensionThe name of the last file opened with the extension removed.
-File.open(path)Creates a new text file and returns a file variable that refers to it. To write to the file, pass the file variable to the print function. Displays a file save dialog box if path is an empty string. The file is closed when the macro exits. Currently, only one file can be open at a time. For an example, refer to the SaveTextFileDemo macro.
-File.openAsString(path)Opens a text file and returns the contents as a string. Displays a file open dialog box if path is an empty string. Use lines=split(str, "\n") to convert the string to an array of lines. See also: File.openUrlAsString.
-File.openAsRawString(path)Opens a file and returns up to the first 5,000 bytes as a string. Returns all the bytes in the file if the name ends with ".txt". Refer to the First10Bytes and ZapGremlins macros for examples.
-File.openAsRawString(path, count)Opens a file and returns up to the first count bytes as a string.
-File.openUrlAsString(url)Opens a URL and returns the contents as a string. Returns an emptly string if the host or file cannot be found. With v1.41i and later, returns "" if there any error, including host or file not found.
-File.openSequence(path, options)Opens the images in the specified directory as a stack. Uses a virtual stack if the 'options' string contains 'virtual'. A filter, image type, start, step, count and scale can also be set, for example "filter=abc bitdepth=32 start=10 step=2 count=10 scale=50". Requires 1.53p.
-File.openDialog(title)Displays a file open dialog and returns the path to the file chosen by the user (example). The macro exits if the user cancels the dialog.
-File.rename(path1, path2)Renames, or moves, a file or directory. Returns "1" (true) if successful.
-File.saveString(string, path)Saves string as a file.
-File.separatorReturns the file name separator character ("/" or "\").
-fill()Fills the image or selection with the current drawing color.
-fillOval(x, y, width, height)Fills an oval bounded by the specified rectangle with the current drawing color. See also: drawOval, setColor, autoUpdate.
-fillRect(x, y, width, height)Fills the specified rectangle with the current drawing color. See also: drawRect, setColor, autoUpdate.
-Fit These functions do curve fitting. The CurveFittingDemo macro demonstrates how to use them.
-Fit.doFit(equation, xpoints, ypoints)Fits the specified equation to the points defined by xpoints, ypoints. Equation can be either the equation name or an index. The equation names are shown in the drop down menu in the Analyze>Tools>Curve Fitting window. With ImageJ 1.42f or later, equation can be a string containing a user-defined equation (example).
-Fit.doFit(equation, xpoints, ypoints, initialGuesses)Fits the specified equation to the points defined by xpoints, ypoints, using initial parameter values contained in initialGuesses, an array equal in length to the number of parameters in equation (example).
-Fit.doWeightedFit(equation, xpoints, ypoints, weights, initialGuesses)Fits the specified equation to the points defined by 'xpoints', 'ypoints', with the weight of each data point given by the 'weights' array. If the error bars of the individual data points are known, the weights should be proportional to 1/error2. The sum of squared residuals is calculated by multiplying each individual (yfit)2 value with the corresponding weight. The 'initialGuesses' array is optional.
-Fit.rSquaredReturns R^2=1-SSE/SSD, where SSE is the sum of the squares of the errors and SSD is the sum of the squares of the deviations about the mean.
-Fit.p(index)Returns the value of the specified parameter.
-Fit.nParamsReturns the number of parameters.
-Fit.f(x)Returns the y value at x (example).
-Fit.nEquationsReturns the number of equations.
-Fit.getEquation(index, name, formula)Returns the name and formula of the specified equation.
-Fit.getEquation(index, name, formula, macroCode)Returns the name, formula and macro code of the specified equation.
-Fit.plotPlots the current curve fit.
-Fit.logResultsCauses doFit() to write a description of the curve fitting results to the Log window.
-Fit.showDialogCauses doFit() to display the simplex settings dialog.
-floodFill(x, y)Fills, with the foreground color, pixels that are connected to, and the same color as, the pixel at (x, y). Does 8-connected filling if there is an optional string argument containing "8", for example floodFill(x, y, "8-connected"). This function is used to implement the flood fill (paint bucket) macro tool.
-floor(n)Returns the largest value that is not greater than n and is equal to an integer. See also: Math.ceil and round.
-fromCharCode(value1, ..., valueN)This function takes one or more Unicode values and returns a string.
-getArgument()Returns the string argument passed to macros called by runMacro(macro, arg), eval(macro), IJ.runMacro(macro, arg) or IJ.runMacroFile(path, arg).
-getBoolean("message")Displays a dialog box containing the specified message and "Yes", "No" and "Cancel" buttons. Returns true (1) if the user clicks "Yes", returns false (0) if the user clicks "No" and exits the macro if the user clicks "Cancel".
-getBoolean(message, yesLabel, noLabel)Displays a dialog box containing the specified message and buttons with custom labels.
-getBoundingRect(x, y, width, height)Replace by getSelectionBounds.
-getCursorLoc(x, y, z, modifiers)Returns the cursor location in pixels and the mouse event modifier flags. The z coordinate is zero for 2D images. For stacks, it is one less than the slice number. Use toScaled(x, y) to scale the coordinates. For examples, see the GetCursorLocDemo and the GetCursorLocDemoTool macros.
-getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec)Returns the current date and time. Note that 'month' and 'dayOfWeek' are zero-based indexes. For an example, refer to the GetDateAndTime macro. See also: getTime.
-getDimensions(width, height, channels, slices, frames)Returns the dimensions of the current image.
-getDirectory(string)Displays a "choose directory" dialog and returns the selected directory, or returns the path to a specified directory, such as "plugins", "home", etc. The returned path ends with the file separator (either "/" or "\" depending on the OS). Returns an empty string if the specified directory is not found or aborts the macro if the user cancels the "choose directory" dialog box. For examples, see the GetDirectoryDemo and ListFilesRecursively macros. See also: getFileList and the File functions.
-getDir(string)An alias of getDirectory since 1.49q. Displays a "choose directory" dialog and returns the selected directory, or returns the path to a specified directory, such as "plugins", "home", etc. The returned path ends with the file separator (either "/" or "\" depending on the OS). Returns an empty string if the specified directory is not found or aborts the macro if the user cancels the "choose directory" dialog box. For examples, see the GetDirectoryDemo and ListFilesRecursively macros. See also: getFileList and the File functions.
-getDir("Choose a Directory")Displays a file open dialog, using the argument as a title, and returns the path to the directory selected by the user.
-getDir("downloads")Returns the path to the Downloads directory.
-getDir("file")Returns the path most recently used to open or save a file.
-getDir("home")Returns the path to the Home directory.
-getDir("image")Returns the path to the directory that the active image was loaded from.
-getDir("imagej")Returns the path to the ImageJ directory.
-getDir("luts")Returns the path to the luts directory.
-getDir("macros")Returns the path to the macros directory.
-getDir("plugins")Returns the path to the plugins directory.
-getDir("startup")Returns the path to the directory that ImageJ was launched from.
-getDir("temp")Returns the path to the temporary directory (/tmp on Linux and Mac OS X).
-getDir("cwd")Returns the path to the current working directory.
-getDir("preferences")Returns the path to the directory containing "IJ_Prefs.txt".
-getDisplayedArea(x, y, width, height)Returns the pixel coordinates of the actual displayed area of the image canvas. For an example, see the Pixel Sampler Tool.
-getFileList(directory)Returns an array containing the names of the files in the specified directory path. The names of subdirectories have a "/" appended. For an example, see the ListFilesRecursively macro.
-getFontList()Returns an array containing the names of available system fonts (example).
-getHeight()Returns the height in pixels of the current image.
-getHistogram(values, counts, nBins[, histMin, histMax])Returns the histogram of the current image or selection. Values is an array that will contain the pixel values for each of the histogram counts (or the bin starts for 16 and 32 bit images), or set this argument to 0. Counts is an array that will contain the histogram counts. nBins is the number of bins that will be used. It must be 256 for 8 bit and RGB image, or an integer greater than zero for 16 and 32 bit images. With 16-bit images, the Values argument is ignored if nBins is 65536. With 16-bit and 32-bit images, the histogram range can be specified using optional histMin and histMax arguments. See also: getStatistics, HistogramLister, HistogramPlotter, StackHistogramLister and CustomHistogram.
-getImageID()Returns the unique ID (a negative number) of the active image. Use the selectImage(id), isOpen(id) and isActive(id) functions to activate an image or to determine if it is open or active.
-getImageInfo()Returns a string containing the text that would be displayed by the Image>Show Info command. To retrieve the contents of a text window, use getInfo("window.contents"). For an example, see the ListDicomTags macros. See also: getMetadata and Property.getInfo.
-getInfo("command.name")Returns the name of the most recently invoked command. The names of commands invoked using keyboard shortcuts are preceded by "^" (example).
-getInfo(DICOM_TAG)Returns the value of a DICOM tag in the form "xxxx,xxxx", e.g. getInfo("0008, 0060"). Returns an empty string if the current image is not a DICOM or if the tag was not found.
-getInfo("font.name")Returns the name of the current font.
-getInfo("image.description")Returns the TIFF image description tag, or an empty string if this is not a TIFF image or the image description is not available.
-getInfo("image.directory")Returns the directory that the current image was loaded from, or an empty string if the directory is not available.
-getInfo("image.filename")Returns the name of the file that the current image was loaded from, or an empty string if the file name is not available.
-getInfo("image.title")Returns the title of the current image. Same as getTitle.
-getInfo("image.subtitle")Returns the subtitle of the current image. This is the line of information displayed above the image and below the title bar.
-getInfo("log")Returns the contents of the Log window, or "" if the Log window is not open.
-getInfo("macro.filepath")Returns the filepath of the most recently loaded macro or script. Use File.getName(getInfo("macro.filepath")) to get the file name and File.getDirectory(getInfo("macro.filepath")) to get the directory.
-getInfo("micrometer.abbreviation")Returns "µm", the abbreviation for micrometer.
-getInfo("os.name")Returns the OS name ("Mac OS X", "Linux" or "Windows").
-getInfo("overlay")Returns information about the current image's overlay.
-getInfo("selection.name")Returns the name of the current selection, or "" if there is no selection or the selection does not have a name. The argument can also be "roi.name". See also: Roi.getName.
-getInfo("selection.color")Returns the color of the current selection. See also: Roi.getStrokeColor.
-getInfo("slice.label")Return the label of the current stack slice. This is the string that appears in parentheses in the subtitle, the line of information above the image. Returns an empty string if the current image is not a stack or the current slice does not have a label.
-getInfo("threshold.method")Returns the current thresholding method ("IsoData", "Otsu", etc).
-getInfo("threshold.mode")Returns the current thresholding mode ("Red", "B&W" or"Over/Under").
-getInfo("window.contents")If the front window is a text window, returns the contents of that window. If the front window is an image, returns a string containing the text that would be displayed by Image>Show Info. Note that getImageInfo() is a more reliable way to retrieve information about an image. Use split(getInfo(), '\n') to break the string returned by this function into separate lines. Replaces the getInfo() function.
-getInfo("window.title")Returns the title of the front-most window. Use getTitle to get the title of the current batch mode image.
-getInfo("window.type")Returns the type ("Image", "Text", "ResultsTable", "Editor", "Plot", "Histogram", etc.) of the front window.
-getInfo(key)Returns the Java property associated with the specified key (e.g., "java.version", "os.name", "user.home", "user.dir", etc.). Returns an empty string if there is no value associated with the key. See also: getList("java.properties").
-getLine(x1, y1, x2, y2, lineWidth)Returns the starting coordinates, ending coordinates and width of the current straight line selection. The coordinates and line width are in pixels. Sets x1 = -1 if there is no line selection. Refer to the GetLineDemo macro for an example. See also: makeLine.
-getList("image.titles")Returns a list (array) of image window titles. For an example, see the DisplayWindowTitles macro.
-getList("window.titles")Returns a list (array) of non-image window titles. For an example, see the DisplayWindowTitles macro.
-getList("java.properties")Returns a list (array) of Java property keys. For an example, see the DisplayJavaProperties macro. See also: getInfo(key).
-getList("threshold.methods")Returns a list of the available automatic thresholding methods (example).
-getList("LUTs")Returns, as an array, a list of the LUTs in the Image>Lookup Tables menu (example).
-getLocationAndSize(x, y, width, height)Returns the location and size, in screen coordinates, of the active image window. Use getWidth and getHeight to get the width and height, in image coordinates, of the active image. See also: setLocation,
-getLut(reds, greens, blues)Returns three arrays containing the red, green and blue intensity values from the current lookup table. See the LookupTables macros for examples.
-getMetadata("Info")Returns the metadata (a string) from the "Info" property of the current image. With DICOM images, this is the information (tags) in the DICOM header. See also: setMetadata and Property.getInfo.
-getMetadata("Label")Returns the current slice label. The first line of the this label (up to 60 characters) is displayed as part of the image subtitle. With DICOM stacks, returns the metadata (tags) from the DICOM header. See also: Property.getSliceLabel and Property.setSliceLabel.
-getMinAndMax(min, max)Returns the minimum and maximum displayed pixel values (display range). See the DisplayRangeMacros for examples.
-getNumber("prompt", defaultValue)Displays a dialog box and returns the number entered by the user. The first argument is the prompting message and the second is the value initially displayed in the dialog. Exits the macro if the user clicks on "Cancel" in the dialog. Returns defaultValue if the user enters an invalid number. See also: Dialog.create.
-getPixel(x, y)Returns the raw value of the pixel at (x, y). Uses bilinear interpolation if 'x' or 'y' are not integers. Use getValue(x, y) to get calibrated pixel values from 8 and 16 bit images and intensity values from RGB images. Note that pixels in RGB images contain red, green and blue components that need to be extracted using shifting and masking. See the Color Picker Tool macro for an example that shows how to do this.
-getPixelSize(unit, pixelWidth, pixelHeight)Returns the unit of length (as a string) and the pixel dimensions. For an example, see the ShowImageInfo macro. See also: getVoxelSize.
-getProfile()Runs Analyze>Plot Profile (without displaying the plot) and returns the intensity values as an array. For an example, see the GetProfileExample macro. See also: Plot.getValues().
-getRawStatistics(nPixels, mean, min, max, std, histogram)This function is similar to getStatistics except that the values returned are uncalibrated and the histogram of 16-bit images has a bin width of one and is returned as a max+1 element array. For examples, refer to the ShowStatistics macro set. See also: calibrate and List.setMeasurements
-getResult("Column", row)Returns a measurement from the ImageJ results table or NaN if the specified column is not found. The first argument specifies a column in the table. It must be a "Results" window column label, such as "Area", "Mean" or "Circ.". The second argument specifies the row, where 0<=rowSet Measurements.
-getSelectionBounds(x, y, width, height)Returns the smallest rectangle that can completely contain the current selection. x and y are the pixel coordinates of the upper left corner of the rectangle. width and height are the width and height of the rectangle in pixels. If there is no selection, returns (0, 0, ImageWidth, ImageHeight). See also: selectionType and setSelectionLocation.
-getSelectionCoordinates(xpoints, ypoints)Returns two arrays containing the X and Y coordinates, in pixels, of the points that define the current selection. See the SelectionCoordinates macro for an example. See also: selectionType, getSelectionBounds.
-getSliceNumber()Returns the number of the currently displayed stack image, an integer between 1 and nSlices. Returns 1 if the active image is not a stack. See also: setSlice, Stack.getPosition.
-getStatistics(area, mean, min, max, std, histogram)Returns the area, average pixel value, minimum pixel value, maximum pixel value, standard deviation of the pixel values and histogram of the active image or selection. The histogram is returned as a 256 element array. For 8-bit and RGB images, the histogram bin width is one. For 16-bit and 32-bit images, the bin width is (max-min)/256. For examples, refer to the ShowStatistics macro set. Note that trailing arguments can be omitted. For example, you can use getStatistics(area), getStatistics(area, mean) or getStatistics(area, mean, min, max). See also: getRawStatistics and List.setMeasurements
-getString("prompt", "default")Displays a dialog box and returns the string entered by the user. The first argument is the prompting message and the second is the initial string value. Exits the macro if the user clicks on "Cancel" or enters an empty string. See also: Dialog.create.
-getStringWidth(string)Returns the width in pixels of the specified string. See also: getValue("font-height"), String.setFontSize, setFont and drawString.
-getThreshold(lower, upper)Returns the lower and upper threshold levels. Both variables are set to -1 if the active image is not thresholded. See also: setThreshold, getThreshold, resetThreshold.
-getTime()Returns the current time in milliseconds. The granularity of the time varies considerably from one platform to the next. On Windows NT, 2K, XP it is about 10ms. On other Windows versions it can be as poor as 50ms. On many Unix platforms, including Mac OS X, it actually is 1ms. See also: getDateAndTime.
-getTitle()Returns the title of the current image.
-getValue(x, y)Returns calibrated pixel values from 8 and 16 bit images and intensity values from RGB images. Uses bilinear interpolation if 'x' or 'y' are not integers. Use getPixel(x, y) to read raw pixel values.
-getValue("color.foreground")Returns the current foreground color as a value that can be passed to the setColor(value) function. The value returned is the pixel value used by the Edit>Fill command and by drawing tools.
-getValue("color.background")Returns the current background color as a value that can be passed to the setColor(value) function. The value returned is the pixel value used by the Edit>Clear command.
-getValue("rgb.foreground")Returns the current foreground color as an RGB pixel value (example).
-getValue("rgb.background")Returns the current background color as an RGB pixel value.
-getValue("font.size")Returns the size, in points, of the current font.
-getValue("font.height")Returns the height, in pixels, of the current font.
-getValue("selection.size")Returns the number of points in the current selection, or 0 if there is no selection. See also: Roi.size.
-getValue("selection.width")Returns the stroke width of the current selection. See also: Roi.getStrokeWidth.
-getValue("results.count")Returns the number of lines in the current results table. Unlike nResults, works with tables that are not named "Results".
-getValue("rotation.angle")Returns the current Image>Transform>Rotate angle.
-getValue("image.size")Returns the size of the current image in bytes.
-getValue("Mean, Median, Feret, etc.")Returns a measurement result, where the argument is "Area", "Mean", "StdDev", "Mode", "Min", "Max", "X", "Y", "XM", "YM", "Perim.", "BX", "BY", "Width", "Height", "Major", "Minor", "Angle", "Circ.", "Feret", "IntDen", "Median", "Skew", "Kurt", "%Area", "RawIntDen", "Ch", "Slice", "Frame", "FeretX", "FeretY", "FeretAngle", "MinFeret", "AR", "Round", "Solidity", "MinThr", "MaxThr" or "Length". Add " raw" to the argument to disable calibration, for example getValue("Mean raw"). Add " limit" to the argument to enable the "limit to threshold" option.
-getVoxelSize(width, height, depth, unit)Returns the voxel size and unit of length ("pixel", "mm", etc.) of the current image or stack. See also: getPixelSize, setVoxelSize.
-getVersion()Returns the ImageJ version number as a string (e.g., "1.34s"). See also: IJ.getFullVersion.
-getWidth()Returns the width in pixels of the current image.
-getZoom()Returns the magnification of the active image, a number in the range 0.03125 to 32.0 (3.1% to 3200%).
-IJ These functions provide access to miscellaneous methods in ImageJ's IJ class.
-IJ.deleteRows(index1, index2)Deletes rows index1 through index2 in the results table.
-IJ.getToolName()Returns the name of the currently selected tool. See also: setTool.
-IJ.getFullVersionReturns the ImageJ version and build number as a string (e.g., "1.52d11").
-IJ.freeMemory()Returns the memory status string (e.g., "2971K of 658MB (<1%)") that is displayed when the users clicks in the ImageJ status bar.
-IJ.checksum("MD5 string", string)Returns the MD5 (or SHA-256) checksum from a string.
-IJ.checksum("MD5 file", filepath)Returns the MD5 (or SHA-256) checksum from a file. If 'filepath' is a directory or invalid, "0" is returned.
-IJ.currentMemory()Returns, as a string, the amount of memory in bytes currently used by ImageJ.
-IJ.log(string)Displays string in the Log window.
-IJ.maxMemory()Returns, as a string, the amount of memory in bytes available to ImageJ. This value (the Java heap size) is set in the Edit>Options>Memory & Threads dialog box.
-IJ.pad(n, length)Pads 'n' with leading zeros and returns the result (example). Note that 'n' can be either a number or a string. See also: String.pad.
-IJ.redirectErrorMessages()Causes next image opening error to be redirected to the Log window and prevents the macro from being aborted (example).
-IJ.renameResults(name)Changes the title of the "Results" table to the string name.
-IJ.renameResults(oldName, newName)Changes the title of a results table from oldName to newName.
-Image Functions for working with the active image, available in ImageJ 1.53f and later.
-Image.title The title of the active image. Requires 1.53h.
-Image.width The width of the active image.
-Image.height The height of the active image.
-Image.copy Copies the contents of the current selection, or the entire image if there is no selection, to the internal clipboard.
-Image.paste(x, y)Inserts the contents of the internal clipboard at the specified location in the active image.
-Image.paste(x, y, mode)Inserts the contents of the internal clipboard at x,y using the specified transfer mode ("Copy", "Blend", "Average", "Difference", "Transparent", "Transparent2", "AND", "OR", "XOR", "Add", "Subtract", "Multiply", or "Divide""Copy", "Blend", "Average", "Difference", "Transparent", "Transparent2", "AND", "OR", "XOR", "Add", "Subtract", "Multiply", or "Divide").
-imageCalculator(operator, img1, img2)Runs the Process>Image Calculator tool, where operator ("add", "subtract", "multiply", "divide", "and", "or", "xor", "min", "max", "average", "difference" or "copy") specifies the operation, and img1 and img2 specify the operands. img1 and img2 can be either an image title (a string) or an image ID (an integer). The operator string can include up to three modifiers: "create" (e.g., "add create") causes the result to be stored in a new window, "32-bit" causes the result to be 32-bit floating-point and "stack" causes the entire stack to be processed. See the ImageCalculatorDemo macros for examples.
-indexOf(string, substring)Returns the index within string of the first occurrence of substring. See also: lastIndexOf, startsWith, endsWith, substring, toLowerCase, replace, matches.
-indexOf(string, substring, fromIndex)Returns the index within string of the first occurrence of substring, with the search starting at fromIndex.
-is("animated")Returns true if the current image is an animated stack.
-is("applet")Returns true if ImageJ is running as an applet.
-is("area")Returns true if the current image has an area selection.
-is("Batch Mode")Returns true if the macro interpreter is running in batch mode.
-is("binary")Returns true if the current image is binary (8-bit with only 0 and 255 values).
-is("Caps Lock Set")Returns true if the caps lock key is set. Always return false on some platforms.
-is("changes")Returns true if the current image's 'changes' flag is set.
-is("composite")Returns true if the current image is a a multi-channel stack that uses the CompositeImage class.
-is("FFT")Returns true if the current image is a Fourier transform image, an 8-bit image showing the logarithm of the power spectrum, with the full Fourier transform data in the background (so you can do an inverse transform).
-is("global scale")Returns true if there is global spatial calibration.
-is("grayscale")Returns true if the current image is grayscale, or an RGB image with identical R, G and B channels.
-is("Inverting LUT")Returns true if the current image is using an inverting (monotonically decreasing) lookup table.
-is("InvertY")Returns true if the 'invertY' property of the active image is enabled.
-is("line")Returns true if the current image has a line selection.
-is("locked")Returns true if the current image is locked.
-is("Virtual Stack")Returns true if the current image is a virtual stack.
-isActive(id)Returns true if the image with the specified ID is active.
-isKeyDown(key)Returns true if the specified key is pressed, where key must be "shift", "alt" or "space". See also: setKeyDown.
-isNaN(n)Returns true if the value of the number n is NaN (Not-a-Number). A common way to create a NaN is to divide zero by zero. Comparison with a NaN always returns false so "if (n!=n)" is equivalent to (isNaN(n))". Note that the numeric constant NaN is predefined in the macro language. The NaNs macro demonstrates how to remove NaNs from an image.
-isOpen(id)Returns true if the image with the specified ID is open.
-isOpen("Title")Returns true if the window with the specified title is open.
-lastIndexOf(string, substring)Returns the index within string of the rightmost occurrence of substring. See also: indexOf, startsWith, endsWith, substring.
-lengthOf(str)Returns the length of a string or array. Can be replaced with str.length (1.52t or later) or arr.length, where is 'str' is a string variable and 'arr' is an array variable.
-lineTo(x, y)Draws a line from current location to (x, y) . See also: Overlay.lineTo.
-List These functions work with a list of key/value pairs. The ListDemo macro demonstrates how to use them.
-List.set(key, value)Adds a key/value pair to the list.
-List.get(key)Returns the string value associated with key, or an empty string if the key is not found.
-List.getValue(key)When used in an assignment statement, returns the value associated with key as a number. Aborts the macro if the value is not a number or the key is not found.
-List.sizeReturns the size of the list.
-List.clear()Resets the list.
-List.setList(list)Loads the key/value pairs in the string list.
-List.getListReturns the list as a string.
-List.setMeasurementsMeasures the current image or selection and loads the resulting keys (Results table column headings) and values into the list. Use List.setMeasurements("limit") to measure using the "Limit to threshold" option. All parameters listed in the Analyze>Set Measurements dialog box are measured, including those that are unchecked. Use List.getValue() in an assignment statement to retrieve the values. See the DrawEllipse macro for an example. With ImageJ 1.52p or later, it is easier to use the getValue() function to get a single measurement value. Examples: getValue("Mean"), getValue("Mean limit") and getValue("Mean raw").
-List.setMeasurements("limit")This is a version of List.setMeasurements that enables the "Limit to threshold" option.
-List.setCommandsLoads the ImageJ menu commands (as keys) and the plugins that implement them (as values).
-List.toArrays(keys, values)Retrieves keys and values as a pair of string arrays, sorted alphabetically for keys.
-List.fromArrays(keys, values)Creates the List from keys and values arrays.
-List.indexOf(key)Returns the alphabetic position of the specified key, or -1 if not found. Note that this function, as well as List.size, returns a string.
-log(n)Returns the natural logarithm (base e) of n. Note that log10(n) = log(n)/log(10). See also: Math.log10.
-makeArrow(x1, y1, x2, y2, style)Creates an arrow selection, where 'style' is a string containing "filled", "notched", "open", "headless" or "bar", plus the optionial modifiers "outline", "double", "small", "medium" and "large" (example). See also: Roi.setStrokeWidth and Roi.setStrokeColor.
-makeEllipse(x1, y1, x2, y2, aspectRatio)Creates an elliptical selection, where x1,y1,x2,y2 specify the major axis of the ellipse and aspectRatio (<=1.0) is the ratio of the lengths of minor and major axis.
-makeLine(x1, y1, x2, y2)Creates a new straight line selection. The origin (0, 0) is assumed to be the upper left corner of the image. Coordinates are in pixels. You can create segmented line selections by specifying more than two coordinate pairs, for example makeLine(25, 34, 44, 19, 69, 30, 71, 56). After creating the selection, use Roi.setStrokeWidth to set the width and Roi.setStrokeColor to set the color.
-makeLine(x1, y1, x2, y2, lineWidth)Creates a straight line selection with the specified width. See also: getLine.
-makeLine(x1, y1, x2, y2, x3, y3, ...)Creates a segmented line selection. After creating the selection, use Roi.setStrokeWidth to set the width and Roi.setStrokeColor to set the color. See also: makeSelection("polyline", xpoints, ypoints).
-makeOval(x, y, width, height)Creates an elliptical selection, where (x, y) define the upper left corner of the bounding rectangle of the ellipse.
-makePoint(x, y, options)Creates a point selection at the specified location, with the type ('hybrd', 'cross', 'dot' or 'circle'), color ('red', 'white', etc.) and size ('tiny', 'small', 'medium', 'large' or 'extra large') of the point defined in the 'options' string (example). The point is added to an overlay if the options string contains 'add'. Create a multi-point selection by using makeSelection("point", xpoints, ypoints). All the makePoint() options ('cross', 'small', 'red', etc.) can be added to first argument.
-makePoint(x, y)Creates a point selection at the specified location. Create a multi-point selection by using makeSelection("point", xpoints, ypoints). Use setKeyDown("shift"); makePoint(x, y); to add a point to an existing point selection.
-makePolygon(x1, y1, x2, y2, x3, y3, ...)Creates a polygonal selection, where at least three coordinate pairs must be specified. As an example, makePolygon(20, 48, 59, 13, 101, 40, 75, 77, 38, 70) creates a polygon selection with five sides. See also: makeSelection("polygon", xpoints, ypoints).
-makeRectangle(x, y, width, height)Creates a rectangular selection, where x and y are the coordinates (in pixels) of the upper left corner of the selection. The origin (0, 0) of the coordinate system is the upper left corner of the image.
-makeRectangle(x, y, width, height, arcSize)Creates a rounded rectangular selection using the specified corner arc size.
-makeRotatedRectangle(x1, y1, x2, y2, width)Creates a rotated rectangular selection, which is similar to a wide line where (x1, y1) is the start of the line, (x2, y2) is the end of the line and 'width' is the line width.
-makeSelection(type, xpoints, ypoints)Creates a selection from a list of XY coordinates. The first argument should be "polygon", "freehand", "polyline", "freeline", "angle" or "point", or the numeric value returned by selectionType. The xpoints and ypoints arguments are numeric arrays that contain the X and Y coordinates. See the MakeSelectionDemo macro for examples. When creating a multi-point selection and using ImageJ 1.52i or later, the first argument can include words that define the type ('hybrd', 'cross', 'dot' or 'circle'), color ('red', 'white', etc.) and size ('tiny', 'small', 'medium', 'large' or 'extra large') of the points (e.g., "point small red cross").
-makeText(string, x, y)Creates a text selection, where x and y are the coordinates (in pixels) of the upper left corner of the selection. The selection will use the font and size specified by the last call to setFont(). The CreateOverlay macro provides an example.
-matches(string, regex)Returns true if string matches the specified regular expression. Can be replaced with string.matches(regex) in ImageJ 1.52t or later. See also: startsWith, endsWith, indexOf, replace.
-Math Functions for performing basic numeric operations, available in ImageJ 1.52u or later.
-Math.abs(n)Returns the absolute value of n.
-Math.acos(n)Returns the inverse cosine (in radians) of n.
-Math.asin(n)Returns the inverse sine (in radians) of n.
-Math.atan(n)Returns the inverse tangent (arctangent) of n, a value in the range -PI/2 through PI/2.
-Math.atan2(y, x)Calculates the inverse tangent of y/x and returns an angle in the range -PI to PI, using the signs of the arguments to determine the quadrant. Multiply the result by 180/PI to convert to degrees.
-Math.ceil(n)Returns the smallest (closest to negative infinity) value that is greater than or equal to n and is an integer.
-Math.cos(angle)Returns the cosine of an angle (in radians).
-Math.erf(x)Returns an approximation of the error function.
-Math.exp(n)Returns the exponential number e (i.e., 2.718...) raised to the power of n.
-Math.floor(n)Returns the largest value that is not greater than n and is equal to an integer.
-Math.log(n)Returns the natural logarithm (base e) of n.
-Math.log10(n)Returns the base 10 logarithm of n.
-Math.min(n1, n2)Returns the smaller of two values.
-Math.max(n1, n2)Returns the larger of two values.
-Math.pow(base, exponent)Returns the value of base raised to the power of exponent.
-Math.round(n)Returns the closest integer to n.
-Math.sin(angle)Returns the sine of an angle (in radians).
-Math.sqr(n)Returns the square of n.
-Math.sqrt(n)Returns the square root of n, or NaN if n is less than zero.
-Math.tan(n)Returns the tangent of an angle (in radians).
-Math.toRadians(degrees)Converts an angle in degrees to an equivalent angle in radians. Requires 1.53f.
-Math.toDegrees(radians)Converts an angle in radians to an equivalent angle in degrees. Requires 1.53f.
-Math.constrain(n, min, max)Limits 'n' to the range 'min'-'max'. Requires 1.53n.
-Math.map(n, low1, high1, low2, high2)Maps the value 'n' in the input range 'low1'-'high1' to the output range 'low2'-'high2'. Requires 1.53n.
-maxOf(n1, n2)Returns the greater of two values. See also: Math.max.
-minOf(n1, n2)Returns the smaller of two values. See also: Math.min.
-moveTo(x, y)Sets the current drawing location. The origin is always assumed to be the upper left corner of the image.
-newArray(size)Returns a new array containing size elements. You can also create arrays by listing the elements, for example newArray(1, 4, 7) or newArray("a", "b", "c"). For more examples, see the Arrays macro. In ImageJ 1.53g or newer, arrays automatically expand in size as needed (example). To use expandable arrays in earlier versions, call setOption("ExpandableArrays", true). The ImageJ macro language does not directly support 2D arrays. As a work around, either create a blank image and use setPixel() and getPixel(), or create a 1D array using a=newArray(xmax*ymax) and do your own indexing (e.g., value=a[x+y*xmax]).
-newImage(title, type, width, height, depth)Opens a new image or stack using the name title. The string type should contain "8-bit", "16-bit", "32-bit" or "RGB". In addition, it can contain "white", "black" or "ramp" (the default is "white"). As an example, use "16-bit ramp" to create a 16-bit image containing a grayscale ramp. Precede with call("ij.gui.ImageWindow.setNextLocation", x, y) to set the location of the new image. Width and height specify the width and height of the image in pixels. Depth specifies the number of stack slices.
-newMenu(macroName, stringArray)Defines a menu that will be added to the toolbar when the menu tool named macroName is installed. Menu tools are macros with names ending in "Menu Tool". StringArray is an array containing the menu commands. Returns a copy of stringArray. For an example, refer to the Toolbar Menus toolset.
-nImages Returns number of open images. The parentheses "()" are optional.
-nResults Returns the current measurement counter value. The parentheses "()" are optional. See also: getValue("results.count").
-nSlices Returns the number of images in the current stack. Returns 1 if the current image is not a stack. The parentheses "()" are optional. See also: getSliceNumber, getDimensions.
-open(path)Opens and displays a tiff, dicom, fits, pgm, jpeg, bmp, gif, lut, roi, or text file. Displays an error message and aborts the macro if the specified file is not in one of the supported formats, or if the file is not found. Displays a file open dialog box if path is an empty string or if there is no argument. Use the File>Open command with the command recorder running to generate calls to this function. With 1.41k or later, opens images specified by a URL, for example open("../../images/clown.gif"). With 1.49v or later, opens a folder of images as a stack. Use open("path/to/folder", "virtual") to open a folder of images as a virtual stack.
-open(path, n)Opens the nth image in the TIFF stack specified by path. For example, the first image in the stack is opened if n=1 and the tenth is opened if n=10.
-Overlay Use these functions to create and manage non-destructive graphic overlays. For an exmple, refer to the OverlayPolygons macro. See also: setColor, setLineWidth and setFont.
-Overlay.moveTo(x, y)Sets the current drawing location.
-Overlay.lineTo(x, y)Draws a line from the current location to (x, y) .
-Overlay.drawLine(x1, y1, x2, y2)Draws a line between (x1, y1) and (x2, y2).
-Overlay.add Adds the drawing created by Overlay.lineTo(), Overlay.drawLine(), etc. to the overlay without updating the display.
-Overlay.setPosition(n)Sets the stack position (slice number) of the last item added to the overlay (example). Set the position to 0 and the item will be displayed on all stack slices.
-Overlay.setPosition(c, z, t)Sets the hyperstack position (channel, slice, frame) of the last item added to the overlay. Set a position to 0 and the item will be displayed on all the corresponding channels, slices or frames.
-Overlay.drawRect(x, y, width, height)Draws a rectangle, where (x, y) specifies the upper left corner.
-Overlay.drawEllipse(x, y, width, height)Draws an ellipse, where (x, y) specifies the upper left corner of the bounding rectangle.
-Overlay.drawString("text", x, y)Draws text at the specified location and adds it to the overlay. The first character is drawn obove and to the right of (x, y). Use setFont() to specify the font and setColor to set specify the color (example).
-Overlay.drawString("text", x, y, angle)Draws text at the specified location and angle and adds it to the overlay (example).
-Overlay.show Displays the current overlay.
-Overlay.hide Hides the current overlay.
-Overlay.hidden Returns true if the active image has an overlay and it is hidden.
-Overlay.remove Removes the current overlay.
-Overlay.clear Resets the overlay without updating the display.
-Overlay.size Returns the size (selection count) of the current overlay. Returns zero if the image does not have an overlay.
-Overlay.addSelection Adds the current selection to the overlay.
-Overlay.addSelection(strokeColor)Sets the stroke color ("red", "green", "ff8800", etc.) of the current selection and adds it to the overlay.
-Overlay.addSelection(strokeColor, strokeWidth)Sets the stroke color ("blue", "yellow", "ffaa77" etc.) and stroke width of the current selection and adds it to the overlay.
-Overlay.addSelection("", 0, fillColor)Sets the fill color ("red", "green", etc.) of the current selection and adds it to the overlay.
-Overlay.activateSelection(index)Activates the specified overlay selection.
-Overlay.activateSelectionAndWait(index)Activates the specified overlay selection and waits for the display to finish updating.
-Overlay.removeSelection(index)Removes the specified selection from the overlay.
-Overlay.update(index)Replaces the overlay selection at 'index' with the current selection. Analogous to roiManager("update").
-Overlay.moveSelection(index, x, y)Moves the specified selection to the specified location.
-Overlay.indexAt(x, y)Returns the index of the last selection in the overlay containing the point (x, y), or an empty string if no selection contains the point. Requires 1.53b.
-Overlay.getBounds(index, x, y, width, height)Returns the bounding rectangle of the selection in the overlay specified by 'index'. Requires 1.53b.
-Overlay.removeRois(name)Removes the selections named 'name' from the overlay. Requires 1.53b.
-Overlay.copy Copies the overlay on the current image to the overlay clipboard.
-Overlay.paste Copies the overlay on the overlay clipboard to the current image.
-Overlay.drawLabels(boolean)Enables/disables overlay labels.
-Overlay.setLabelFontSize(size, options)Sets the label font size. The options string can contain 'scale' (enlarge labels when image zoomed), 'bold' (display bold labels) or 'back' (display labels with contrasting background color.
-Overlay.setLabelColor(color)Sets the color used to draw labels.
-Overlay.useNamesAsLabels(boolean)Controls whether ROI names or index numbers are used as labels.
-Overlay.selectable(false)Prevents the selections in this overlay from being activated by clicking on their labels or by long clicking. Requires 1.51r.
-Overlay.measure Measures all the selections in the current overlay.
-Overlay.setStrokeColor(color)Sets the stroke color all the selections in the current overlay.
-Overlay.setStrokeWidth(width)Sets the stroke width all the selections in the current overlay.
-Overlay.flatten Creates a new RGB image that has the overlay rendered as pixel data.
-Overlay.cropAndSave(dir, format)Saves the contents of the overlay selections as separate images, where 'dir' is the directory path and 'format' is "tif", "png" or "jpg". Set 'format' to "show" and the images will be displayed in a stack and not saved. Requires 1.53d.
-Overlay.fill(color)Fills all the selections in the overlay with 'color'. Requires 1.53h.
-Overlay.fill(color1, color2)Fills all the selections in the overlay with 'color1' after clearing the image to 'color2'. Requires 1.53h.
-Overlay.xor(array)Creates a selection that is the result of XORing all the selections in the overlay that have an index in 'array'. Requires 1.53h.
-parseFloat(string)Converts the string argument to a number and returns it. Returns NaN (Not a Number) if the string cannot be converted into a number. Use the isNaN() function to test for NaN. For examples, see ParseFloatIntExamples.
-parseFloat("Infinity")Returns the special floating point value representing +Infinity.
-parseFloat("-Infinity")Returns the special floating point value representing -Infinity.
-parseFloat("NaN")Returns the special floating point value representing NaN (not a number).
-parseInt(string)Converts string to an integer and returns it. Returns NaN if the string cannot be converted into a integer.
-parseInt(string, radix)Converts string to an integer and returns it. The optional second argument (radix) specifies the base of the number contained in the string. The radix must be an integer between 2 and 36. For radixes above 10, the letters of the alphabet indicate numerals greater than 9. Set radix to 16 to parse hexadecimal numbers. Returns NaN if the string cannot be converted into a integer. For examples, see ParseFloatIntExamples.
-PI Returns the constant π (3.14159265), the ratio of the circumference to the diameter of a circle.
-Plot Use these functions to generate and display plots. For examples, check out the Example Plot, More Example Plots, AdvancedPlots, Semi-log Plot and Arrow Plot macros.
-Plot.create("Title", "X-axis Label", "Y-axis Label", xValues, yValues)Generates a plot using the specified title, axis labels and X and Y coordinate arrays. If only one array is specified it is assumed to contain the Y values and a 0..n-1 sequence is used as the X values. It is also permissible to specify no arrays and use Plot.setLimits() and Plot.add() to generate the plot. Use Plot.show() to display the plot in a window, or it will be displayed automatically when the macro exits.
-Plot.create("Title", "{cat1, cat2, cat3}", "Y-axis Label")Draws category labels instead of x-axis numbers 0, 1, 2.
-Plot.add(type, xValues, yValues)Adds a curve, set of points or error bars to a plot created using Plot.create(). If only one array is specified it is assumed to contain the Y values and a 0..n-1 sequence is used as the X values. The first argument (type) can be "line", "connected circle", "filled", "bar", "separated bar", "circle", "box", "triangle", "diamond", "cross", "x", "dot", "error bars" (in y direction) or "xerror bars". Run Help>Examples>Plots>Plot Styles to see examples. Error bars (supplied by an optional fourth argument) apply to the last dataset provided by Plot.create or Plot.add.
-Plot.add(type, xValues, yValues, label)Adds a curve or set of points to the plot and sets the dataset label used by Plot.showValuesWithLabels.
-Plot.addHistogram(values, binWidth, binCenter)Creates a 'staircase' histogram from array 'values'. If 'binWidth' is 0, automatic binning is applied. 'binCenter' is optional with default=0. BinCenter can, for example, be set to an expected symmetry point for avoiding artificial asymmetry.
-Plot.drawVectors(xStarts, yStarts, xEnds, yEnds)Draws arrows from the starting to ending coordinates contained in the arrays.
-Plot.drawLine(x1, y1, x2, y2)Draws a line between x1,y1 and x2,y2, using the coordinate system defined by Plot.setLimits().
-Plot.drawNormalizedLine(x1, y1, x2, y2)Draws a line using a normalized 0-1, 0-1 coordinate system, with (0, 0) at the top left and (1, 1) at the lower right corner.
-Plot.addText("A line of text", x, y)Adds text to the plot at the specified location, where (0, 0) is the upper left corner of the the plot frame and (1, 1) is the lower right corner. Call Plot.setJustification() to have the text centered or right justified. Plot.setLimits(xMin, xMax, yMin, yMax)Sets the range of the x-axis and y-axis of plots. With version 1.50g and later, when 'NaN' is used as a limit, the range is calculated automatically from the plots that have been added so far.
-Plot.getLimits(xMin, xMax, yMin, yMax)Returns the current axis limits. Note that min>max if the axis is reversed.
-Plot.setLimitsToFit()Sets the range of the x and y axes to fit all data.
-Plot.setColor(color)Specifies the color used in subsequent calls to Plot.add() or Plot.addText(). The argument can be "black", "blue", "cyan", "darkGray", "gray", "green", "lightGray", "magenta", "orange", "pink", "red", "white", "yellow", or a hex value like "#ff00ff". Note that the curve specified in Plot.create() is drawn last.
-Plot.setColor(color1, color2)This is a two argument version of Plot.setColor, where the second argument is used for filling symbols or as the line color for connected points.
-Plot.setBackgroundColor(color)Sets the background color of the plot frame (example).
-Plot.setLineWidth(width)Specifies the width of the line used to draw a curve. Symbols (circle, box, etc.) are also drawn larger if a line width greater than one is specified. Note that the curve specified in Plot.create() is the last one drawn before the plot is displayed or updated.
-Plot.setJustification("center")Specifies the justification used by Plot.addText(). The argument can be "left", "right" or "center". The default is "left".
-Plot.setLegend("label1\tlabel2...", "options")Creates a legend for each of the data sets added with Plot.create and Plot.add. In the first argument, the labels for the data sets should be separated with tab or newline characters. The optional second argument can contain the legend position ("top-left", "top-right", "bottom-left", "bottom-right"; default is automatic positioning), "bottom-to-top" for reversed sequence of the labels, and "transparent" to make the legend background transparent.
-Plot.setFrameSize(width, height)Sets the plot frame size in pixels, overriding the default size defined in the Edit>Options>Profile Plot Options dialog box.
-Plot.getFrameBounds(x, y, width, height)Returns the plot frame bounds.
-Plot.setLogScaleX(boolean)Sets the x axis scale to Logarithmic, or back to linear if the optional boolean argument is false. In versions up to 1.49s, it must be called immediately after Plot.create and before Plot.setLimits. See the LogLogPlot macro for an example.
-Plot.setLogScaleY(boolean)Sets the y axis scale to Logarithmic, or back to linear if the optional boolean argument is false.
-Plot.setXYLabels("x Label", "y Label")Sets the axis labels.
-Plot.setFontSize(size, "options")Sets the default font size in the plot (otherwise specified in Profile Plot Options), used e.g. for axes labels. Can be also called prior to Plot.addText. The optional second argument can include "bold" and/or "italic".
-Plot.setAxisLabelSize(size, "options")Sets the fort size of the axis labels. The optional second argument can include "bold" and/or "italic".
-Plot.setFormatFlags("11001100001111")Controls whether to draw axes labels, grid lines and ticks (major/minor/ticks for log axes). Use the macro recorder and More>>Axis Options in any plot window to determine the binary code.
-Plot.setStyle(index, styleString)Set the style of the plot object (curve, label, etc.) with the specified index, using a comma-delimiterd string ("color1, color2, line width, symbol"). For an example, run the Help>Examples>Plots>Plot Styles command.
-Plot.freeze(boolean)Freezes or unfreezes the plot. In the frozen state, the plot cannot be resized or updated. In the unfrozen state, the plot cannot be tiled.
-Plot.setOptions(string)Sets options for the plot. Multiple options may be separated by whitespace or commas. Note that whitespace surrounding the '=' characters is not allowed. Currently recognized options are: "addhspace=10 addvspace=5"Increases the left and right or top and bottom margins by the given number of pixels. "xinterval=30 yinterval=90"Sets interval between numbers, major ticks and grid lines (default intervals are used if the custom intervals would be too dense or too sparse)"xdecimals=2 ydecimals=-1"Sets the minimum number of decimals; use negative numbers for scientific notation. "msymbol=' \\u00d7"Sets multiplication symbol for scientific notation, here a cross with spaces. For an example, run the Help>Examples>Plots>Plot Results command. Requires 1.53a.
-Plot.replace(index, type, xValues, yValues)Replaces the plot object (curve, Label, etc.) with the specified index by points or a curve as specified in Plot.add(type, xValues, yValues).
-Plot.useTemplate("plot name" or id)Transfers the formatting of an open plot window to the current plot.
-Plot.makeHighResolution(factor)Creates a high-resolution image of the plot enlarged by factor. Add the second argument "disable" to avoid antialiased text.
-Plot.appendToStack Appends the current plot to a virtual stack and resets. Must be called before Plot.show. For an example, run Help>Examples>Plots>Dynamic Plot.
-Plot.show()Displays the plot generated by Plot.create(), Plot.add(), etc. in a window. This function is automatically called when a macro exits.
-Plot.update()Draws the plot generated by Plot.create(), Plot.add(), etc. in an existing plot window. Equivalent to Plot.show if no plot window is open.
-Plot.getValues(xpoints, ypoints)Returns the values displayed by clicking on "List" in a plot or histogram window (example).
-Plot.showValues()Displays the plot values in the Results window using simple "X , Y, X1, Y1, .." column headings. Must be preceded by Plot.show.
-Plot.showValuesWithLabels()Displays the plot values in the Results window using the dataset labels, for example the labels supplied by Plot.setLegend. Must be preceded by Plot.show.
-Plot.drawGrid()Redraws the grid above previous plots.
-Plot.drawShapes("rectangles", lefts, tops, rights, bottoms)Draws one or more rectangles. The four arguments (values or arrays) hold rectangle coordinates.
-Plot.drawBoxes("boxes width=30", x, y1, y2, y3, y4, y5)Draws a boxplot, where 'width' is in pixels, array 'x' holds x-positions and arrays 'y1'..'y5' hold the quartile borders in ascending order. Secondary color will fill the box. For horizontal boxes, use "boxesx width=30" instead.
-Plot.removeNaNs()Removes NaN values from the plot. This has two effects: a) Numerical output via "List" or macro will be free of NaNs; b) Line plots that were interrupted by NaNs are now connected.
-Plot.eneableLive(boolean)Enables and disables the "Live" mode of the active plot. Requires 1.54e.
-pow(base, exponent)Returns the value of base raised to the power of exponent.
-print(string)Outputs a string to the "Log" window. Numeric arguments are automatically converted to strings. The print() function accepts multiple arguments. For example, you can use print(x, y, width, height) instead of print(x+" "+y+" "+width+" "+height). If the first argument is a file handle returned by File.open(path), then the second is saved in the refered file (see SaveTextFileDemo). Numeric expressions are automatically converted to strings using four decimal places, or use the d2s function to specify the decimal places. For example, print(2/3) outputs "0.6667" but print(d2s(2/3, 1)) outputs "0.7".
-The print() function accepts commands such as "\\Clear", "\\Update:" and "\\Update:" (for n<26) that clear the "Log" window and update its contents. For example, print("\\Clear") erases the Log window, print("\\Update:new text") replaces the last line with "new text" and print("\\Update8:new 8th line") replaces the 8th line with "new 8th line". Refer to the LogWindowTricks macro for an example.
-The second argument to print(arg1, arg2) is appended to a text window or table if the first argument is a window title in brackets, for example print("[My Window]", "Hello, world"). With text windows, newline characters ("\n") are not automatically appended and text that starts with "\\Update:" replaces the entire contents of the window. Refer to the PrintToTextWindow, Clock and ProgressBar macros for examples.
-The second argument to print(arg1, arg2) is appended to a table (e.g., ResultsTable) if the first argument is the title of the table in brackets. Use the Plugins>New command to open a blank table. Any command that can be sent to the "Log" window ("\\Clear", "\\Update:" , etc.) can also be sent to a table. Refer to the SineCosineTable2 and TableTricks macros for examples.
-Property Functions for reading and writing image properties, available in ImageJ 1.53a or later.
-Property.get(key)Returns the image property (a string) associated with key, or an empty string if key is not found.
-Property.getNumber(key)Returns the image property associated with key, as a number, or returns NaN if key is not found or the property cannot be converted into a number. Requires 1.53b.
-Property.set(key, property)Adds a key-value pair to the property list of the current image. key must be a string but property can be either a string or a number. The key-value pair is removed if property is an empty string. Add a "ShowInfo" property (e.g. Property.set("ShowInfo", "true")) and the property list will be displayed by the Image>Show Info command (requires 1.53b). The property list is persistent when the image is saved in TIFF format.
-Property.getInfo()Returns the image "info" property string (e.g. DICOM tags or Bio-Formats metadara), or an empty string if there is no "Info" property.
-Property.getSliceLabel Returns the current slice label. The first line of the label (up to 60 characters) is displayed as part of the image subtitle. With DICOM stacks, returns the DICOM header metadata (tags).
-Property.setSliceLabel(string, slice)Sets string as the label of the specified stack slice, were 1<=slice<=nslices. The first 60 characters, up to the first newline, of the label are displayed as part of the image subtitle. Slice labels are saved in the TIFF header.
-Property.setSliceLabel(string)Sets string as the label of the current stack slice.
-Property.getList Returns the properties as a string (e.g. "key1=value1\nkey2=value2"). Requires 1.53b.
-Property.setList(string)Sets the properties from the key/value pairs in 'string'. Requires 1.53b.
-random Returns a uniformly distributed pseudorandom number between 0 and 1.
-random("gaussian")Returns a Gaussian ("normally") distributed pseudorandom number with mean 0.0 and standard deviation 1.0.
-random("seed", seed)Sets the seed (a whole number) used by the random() and random("gaussian") functions. Set a specific seed to get a reproducible pseudorandom sequence.
-rename(name)Changes the title of the active image to the string name.
-replace(string, old, new)Returns a string that results from replacing all occurrences of old in string with new, where old is a single character string. If old is longer than one character, each substring of string that matches the regular expression old is replaced with new. When doing a simple string replacement, and old contains regular expression metacharacters ('.', '[', ']', '^', '$', etc.), you must escape them with a "\\". For example, to replace "[xx]" with "yy", use string=replace(string, "\\[xx\\]", "yy"). Can be replaced with string.replace(old, new) in ImageJ 1.52t or later. See also: matches.
-requires("1.29p")Display a message and aborts the macro if the ImageJ version is less than the one specified. See also: getVersion.
-reset Restores the backup image created by the snapshot function. Note that reset() and run("Undo") are basically the same, so only one run() call can be reset.
-resetMinAndMax With 16-bit and 32-bit images, resets the minimum and maximum displayed pixel values (display range) to be the same as the current image's minimum and maximum pixel values. With 8-bit images, sets the display range to 0-255. With RGB images, does nothing. See the DisplayRangeMacros for examples.
-resetThreshold Disables thresholding. See also: setThreshold, setAutoThreshold, getThreshold.
-restoreSettings Restores Edit>Options submenu settings saved by the saveSettings function.
-ROI Use these functions to get information about the current selection or to get or set selection properties. Refer to the RoiFunctionsDemo macro for examples.
-Roi.size Returns the size of the current selection in points.
-Roi.contains(x, y)Returns true if the point x,y is inside the current selection. Aborts the macro if there is no selection. See also: Roi.getContainedPoints and selectionContains.
-Roi.getBounds(x, y, width, height)Returns the location and size of the selection's bounding rectangle.
-Roi.getFloatBounds(x, y, width, height)Returns the location and size of the selection's bounding rectangle as real numbers.
-Roi.getCoordinates(xpoints, ypoints)Returns, as two arrays, the x and y coordinates that define this selection.
-Roi.getContainedPoints(xpoints, ypoints)Returns, as two arrays, the x and y coordinates of the pixels inside the current selection. Aborts the macro if there is no selection.
-Roi.getDefaultColor Returns the current default selection color as a string.
-Roi.getStrokeColor Returns the selection stroke color as a string.
-Roi.getFillColor Returns the selection fill color as a string.
-Roi.getName Returns the selection name or an empty string if the selection does not have a name.
-Roi.getProperty(key)Returns the value (a string) associated with the specified key or an empty string if the key is not found.
-Roi.setProperty(key, value)Adds the specified key and value pair to the selection properties. Assumes a value of "1" (true) if there is only one argument.
-Roi.getProperties Returns all selection properties or an empty string if the selection does not have properties.
-Roi.getSplineAnchors(x, y)Returns the x and y coordinates of the anchor points of a spline fitted selection (example).
-Roi.setPolygonSplineAnchors(x, y)Creates or updates a spline fitted polygon selection (example).
-Roi.setPolylineSplineAnchors(x, y)Creates or updates a spline fitted polyline selection (example).
-Roi.getType Returns, as a string, the type of the current selection.
-Roi.move(x, y)Moves the selection to the specified location.
-Roi.translate(dx, dy)Translates the selection by 'dx' and 'dy'. Requires 1.53v.
-Roi.setStrokeColor(color)Sets the selection stroke color ("red", "5500ff00". etc.).
-Roi.setStrokeColor(red, green, blue)Sets the selection stroke color, where 'red', 'green' and 'blue' are integers (0-255).
-Roi.setStrokeColor(rgb)Sets the selection stroke color, where 'rgb' is an integer.
-Roi.setFillColor(color)Sets the selection fill color ("red", "5500ff00". etc.). With 1.54e and later, set the stroke color after setting the fill color to both fill and outline the selection.
-Roi.setFillColor(red, green, blue)Sets the selection fill color, where 'red', 'green' and 'blue' are integers (0-255). With 1.54e and later, set the stroke color after setting the fill color to both fill and outline the selection.
-Roi.setFillColor(rgb)Sets the selection fill color, where 'rgb' is an integer. With 1.54e and later, set the stroke color after setting the fill color to both fill and outline the selection.
-Roi.setAntiAlias(boolean)Controls whether anti-aliasing is used when drawing selections (example).
-Roi.setName(name)Sets the selection name.
-Roi.setStrokeWidth(width)Sets the selection stroke width.
-Roi.setUnscalableStrokeWidth(width)Sets the width of the line used to draw this selection and prevents the width from increasing when the image is zoomed. Requires 1.53p.
-Roi.getStrokeWidth Returns the stroke width of the current selection.
-Roi.setGroup(group)Sets the group (a positive number) of the current selection. Zero sets the group to "none". See also: RoiManager.selectGroup and RoiManager.setGroup.
-Roi.getGroupReturns the group (a positive number) of the current selection, or zero if the selection is not in a group.
-Roi.setDefaultGroup(group)Sets the default group (a positive number) of the current selection. Zero sets the default group to "none".
-Roi.getDefaultGroupReturns the default group (a positive number) of the current selection, or zero if the selection is not in a group.
-Roi.setPosition(slice)Sets the selection position. Requires 1.53b.
-Roi.setPosition(channel, slice, frame)Sets the selection position.
-Roi.getPosition(channel, slice, frame)Returns the selection position.
-Roi.getPointPosition(index)Returns the stack position of the point with the specified index in the current point selection.
-Roi.setJustification(str)Sets the justification ("left", "center" or "right") of the current text selection. Requires 1.53b.
-Roi.setFontSize(size)Sets the font size (in points) of the current text selection. Requires 1.53b.
-Roi.getGroupNamesReturns the group names as a comma-delimeted string. Requires 1.53b.
-Roi.setGroupNames(string)Sets the group names from a comma-delimeted string. Requires 1.53b.
-Roi.remove Deletes the selection, if any, from the active image.
-Roi.selectNone Removes the current selection. Requires 1.53v15.
-Roi.copy Copies the selection on the active image to the selection clipboard. Requires 1.53u.
-Roi.paste Copies the selection on the selection clipboard to the active image. Requires 1.53u.
-Roi.getFeretPoints(xpoints, ypoints)Creates new x and y arrays with the end points of the MaxFeret in array elements [0],[1] and MinFeret in [2],[3] (example).
-ROI Manager These function run ROI Manager commands. The ROI Manager is opened if it is not already open. Use roiManager("reset") to delete all ROIs on the list. Use setOption("Show All", boolean) to enable/disable "Show All" mode. Additional ROI Manager Functions. For examples, refer to the RoiManagerMacros, ROI Manager Stack Demo and RoiManagerSpeedTest macros.
-roiManager("and")Uses the conjunction operator on the selected ROIs, or all ROIs if none are selected, to create a composite selection.
-roiManager("add")Adds the current selection to the ROI Manager.
-roiManager("add & draw")Outlines the current selection and adds it to the ROI Manager.
-roiManager("combine")Uses the union operator on the selected ROIs to create a composite selection. Combines all ROIs if none are selected.
-roiManager("count")Returns the number of ROIs in the ROI Manager list. See also: RoiManager.size and RoiManager.selected.
-roiManager("delete")Deletes the selected ROIs from the list, or deletes all ROIs if none are selected.
-roiManager("deselect")Deselects all ROIs in the list. When ROIs are deselected, subsequent ROI Manager commands are applied to all ROIs.
-roiManager("draw")Draws the selected ROIs, or all ROIs if none are selected, using the equivalent of the Edit>Draw command.
-roiManager("fill")Fills the selected ROIs, or all ROIs if none are selected, using the equivalent of the Edit>Fill command.
-roiManager("index")Returns the index of the currently selected ROI on the list, or -1 if the list is empty or no ROIs are selected. Returns the index of the first selected ROI if more than one is selected
-roiManager("measure")Measures the selected ROIs, or if none is selected, all ROIs on the list.
-roiManager("multi measure")Measures all the ROIs on all slices in the stack, creating a Results Table with one row per slice.
-roiManager("multi-measure append")Measures all the ROIs on all slices in the stack, appending the measurements to the Results Table, with one row per slice.
-roiManager("multi-measure one")Measures all the ROIs on all slices in the stack, creating a Results Table with one row per measurement.
-roiManager("multi plot")Plots the selected ROIs, or all ROIs if none are selected, on a single graph.
-roiManager("open", file-path)Opens a .roi file and adds it to the list or opens a ZIP archive (.zip file) and adds all the selections contained in it to the list.
-roiManager("remove slice info")Removes the information in the ROI names that associates them with particular stack slices.
-roiManager("rename", name)Renames the selected ROI. You can get the name of an ROI on the list using RoiManager.getName.
-roiManager("reset")Deletes all ROIs on the list.
-roiManager("save", file-path)Saves all the ROIs on the list in a ZIP archive.
-roiManager("save selected", file-path)Saves the selected ROI as a .roi file.
-roiManager("select", index)Selects an item in the ROI Manager list, where index must be greater than or equal zero and less than the value returned by roiManager("count"). Note that macros that use this function sometimes run orders of magnitude faster in batch mode. Use roiManager("deselect") to deselect all items on the list. For an example, refer to the ROI Manager Stack Demo macro. See also: RoiManager.select and RoiManager.selectByName.
-roiManager("select", indexes)Selects multiple items in the ROI Manager list, where indexes is an array of integers, each of which must be greater than or equal to 0 and less than the value returned by roiManager("count"). The selected ROIs are not highlighted in the ROI Manager list and are no longer selected after the next ROI Manager command is executed.
-roiManager("show all")Displays all the ROIs as an overlay.
-roiManager("show all with labels")Displays all the ROIs as an overlay, with labels.
-roiManager("show all without labels")Displays all the ROIs as an overlay, without labels.
-roiManager("show none")Removes the ROI Manager overlay.
-roiManager("size")Returns the number of ROIs in the ROI Manager list.
-roiManager("sort")Sorts the ROI list in alphanumeric order.
-roiManager("split")Splits the current selection (it must be a composite selection) into its component parts and adds them to the ROI Manager.
-roiManager("update")Replaces the selected ROI on the list with the current selection.
-Additional ROI Manager These functions for working with the ROI Manager are available in ImageJ 1.52u and later.
-RoiManager.multiCrop(dir, options)If 'options' contains "save", saves the contents of the selected ROIs in TIFF format as separate images, where 'dir' is the directory path. Add " png" or " jpg" to save in PNG or JPEG format. Add ' show' and the images will be displayed in a stack. Requires 1.53d.
-RoiManager.getName(index)Returns the name of the selection with the specified index, or an empty string if the selection does not have a name.
-RoiManager.getIndex(name)Returns the index of the first selection with the specified name, or -1 if no selection has that name. Requires 1.53s.
-RoiManager.rotate(angle)rotates the selected selections by 'angle'. Requires 1.53s.
-RoiManager.rotate(angle, xcenter, ycenter)Rotates the selected selections by 'angle', around 'xcenter' and 'ycenter'. Requires 1.53s.
-RoiManager.scale(xscale, yscale, centered)Scales the selected selections by 'xscale' and 'yscale'. Uses the center of the image as the origin if 'centered' is true. Requires 1.53s.
-RoiManager.select(index)Activates the selection at the specidied index.
-RoiManager.selectByName(name)Activates the selection with the specified name. Requires 1.53s.
-RoiManager.selected Returns the number of selected ROIs in the ROI Manager list. Requires 1.53e. See also: RoiManager.size
-RoiManager.selectGroup(group)Selects all ROIs in the ROI Manager that belong to group.
-RoiManager.selectPosition(c, z, t)Selects all ROIs in the ROI Manager that are at the specified position. As an example, to select all ROIs in a stack positioned at slice 5, use RoiManager.selectPosition(0, 5, 0). Requires 1.54d.
-RoiManager.setGroup(group)Sets the group of the selected ROIs. See also: Roi.setGroup, Roi.getGroup, Roi.setDefaultGroup and Roi.getDefaultGroup.
-RoiManager.setPosition(slice)Sets the position of the selected selections.
-RoiManager.setPosition(channel, slice, frame)Sets the position of the selected selections. Requires 1.54g.
-RoiManager.size Returns the number of ROIs in the ROI Manager list. See also: RoiManager.selected
-RoiManager.translate(dx, dy)Translates the selected selections by 'dx' and 'dy'. Requires 1.53s.
-RoiManager.associateROIsWithSlices(boolean)Sets the "Associate 'Show all' ROIs with slices" option. Requires 1.54a.
-RoiManager.restoreCentered(boolean)Sets the "Restore ROIs centered" option. Requires 1.54a.
-RoiManager.useNamesAsLabels(boolean)Sets the "Use ROI names as labels" option. Requires 1.54a.
-round(n)Returns the closest integer to n. See also: floor.
-run(command)Executes an ImageJ menu command. Use the Command Recorder (Plugins>Macros>Record) to generate run() function calls.
-run(command, options)Executes an ImageJ menu command with arguments. The 'options' string contains values that are automatically entered into dialog boxes (must be GenericDialog or OpenDialog). Use the Command Recorder (Plugins>Macros>Record) to generate run() function calls. Use string concatenation to pass a variable as an argument. With ImageJ 1.43 and later, variables can be passed without using string concatenation by adding "&" to the variable name. For examples, see the ArgumentPassingDemo macro. Plugins can directly retrieve the 'options' string by calling Macro.getOptions().
-runMacro(name)Runs the specified macro or script, which is assumed to be in the Image macros folder. A full file path may also be used. Returns any string argument returned by the macro or the last expression evaluated in the script. For an example, see the CalculateMean macro. See also: eval.
-runMacro(name, arg)Runs the specified macro or script, which is assumed to be in the macros folder, or use a full file path. The string argument 'arg' can be retrieved by the macro or script using the getArgument() function. Returns the string argument returned by the macro or the last expression evaluated in the script. See also: getArgument.
-save(path)Saves an image, lookup table, selection or text window to the specified file path. The path must end in ".tif", ".jpg", ".gif", ".zip", ".raw", ".avi", ".bmp", ".fits", ".png", ".pgm", ".lut", ".roi" or ".txt".
-saveAs(format, path)Saves the active image, lookup table, selection, measurement results, selection XY coordinates or text window to the specified file path. The format argument must be "tiff", "jpeg", "gif", "zip", "raw", "avi", "bmp", "fits", "png", "pgm", "text image", "lut", "selection", "results", "xy Coordinates" or "text". Use saveAs(format) to have a "Save As" dialog displayed.
-saveSettings()Saves most Edit>Options submenu settings so they can be restored later by calling restoreSettings.
-screenHeight Returns the screen height in pixels. See also: getLocationAndSize, setLocation.
-screenWidth Returns the screen width in pixels.
-selectionContains(x, y)Returns true if the point x,y is inside the current selection. Aborts the macro if there is no selection. See also: Roi.contains
-selectionName Returns the name of the current selection, or an empty string if the selection does not have a name. Aborts the macro if there is no selection. See also: Roi.getName, Roi.setName, setSelectionName and selectionType.
-selectionType Returns the selection type, where 0=rectangle, 1=oval, 2=polygon, 3=freehand, 4=traced, 5=straight line, 6=segmented line, 7=freehand line, 8=angle, 9=composite and 10=point. Returns -1 if there is no selection. For an example, see the ShowImageInfo macro. See also: Roi.getType,
-selectImage(id)Activates the image with the specified ID (a negative number). If id is greater than zero, activates the idth image listed in the Window menu. The id can also be an image title (a string).
-selectWindow("name")Activates the window with the title "name".
-setAutoThreshold()Uses the "Default" method to determine the threshold. It may select dark or bright areas as thresholded, as was the case with the Image>Adjust>Threshold "Auto" option in ImageJ 1.42o and earlier. See also: setThreshold, getThreshold, resetThreshold.
-setAutoThreshold(method)Uses the specified method to set the threshold levels of the current image. Use the getList("threshold.methods") function to get a list of the available methods. Add " dark" to the method name if the image has a dark background. Add " 16-bit" to use the full 16-bit histogram when calculating the threshold of 16-bit images. Add " stack" to use histogram of the entire stack when calculating the threshold. For an example, see the AutoThresholdingDemo macro.
-setBackgroundColor(r, g, b)Sets the background color, where r, g, and b are >= 0 and <= 255. See also: setForegroundColor.
-setBackgroundColor(rgb)Sets the background color, where rgb is an RGB pixel value. See also: getValue("rgb.background").
-setBatchMode(arg)Controls whether images are visible or hidden during macro execution. If arg is 'true', the interpreter enters batch mode and newly opened images are not displayed. If arg is 'false', exits batch mode and disposes of all hidden images except for the active image, which is displayed in a window. The interpreter also exits batch mode when the macro terminates, disposing of all hidden images.
-With ImageJ 1.48h or later, you can use 'show' and 'hide' arguments to individually show or hide images. By not displaying and updating images, batch mode macros run up to 20 times faster. Examples: BatchModeTest, BatchMeasure, BatchSetScale and ReplaceRedWithMagenta.
-setBatchMode("exit and display")Exits batch mode and displays all hidden images.
-setBatchMode("show")Displays the active hidden image, while batch mode remains in same state.
-setBatchMode("hide")Enters (or remains in) batch mode and hides the active image
-setColor(r, g, b)Sets the drawing color, where r, g, and b are >= 0 and <= 255. With 16 and 32 bit images, sets the color to 0 if r=g=b=0. With 16 and 32 bit images, use setColor(1, 0, 0) to make the drawing color the same is the minimum displayed pixel value. SetColor() is faster than setForegroundColor(), and it does not change the system wide foreground color or repaint the color picker tool icon, but it cannot be used to specify the color used by commands called from macros, for example run("Fill"). See also: Color.set.
-setColor(value)Sets the drawing color. For 8 bit images, 0<=value<=255. For 16 bit images, 0<=value<=65535. For RGB images, use hex constants (e.g., 0xff0000 for red). This function does not change the foreground color used by run("Draw") and run("Fill").
-setColor(string)Sets the drawing color, where 'string' can be "black", "blue", "cyan", "darkGray", "gray", "green", "lightGray", "magenta", "orange", "pink", "red", "white", "yellow", or a hex value like "#ff0000".
-setFont(name, size[, style])Sets the font used by the drawString function. The first argument is the font name. It should be "SansSerif", "Serif" or "Monospaced". The second is the point size. The optional third argument is a string containing "bold" or "italic", or both. The third argument can also contain the keyword "antialiased". With ImageJ 1.54e and newer, text antialiasing is enabled by default and you have to use the keyword 'no-smoothing' to display non-antialiased text. For examples, run the TextDemo macro.
-setFont("user")Sets the font to the one defined in the Edit>Options>Fonts window. See also: getInfo("font.name"), getValue("font.size") and getValue("font.height").
-setForegroundColor(r, g, b)Sets the foreground color, where r, g, and b are >= 0 and <= 255. See also: Color.setForeground. setColor and setBackgroundColor.
-setForegroundColor(rgb)Sets the foreground color, where rgb is an RGB pixel value. See also: getValue("rgb.foreground").
-setJustification("center")Specifies the justification used by drawString() and Plot.addText(). The argument can be "left", "right" or "center". The default is "left".
-setKeyDown(keys)Simulates pressing the shift, alt or space keys, where keys is a string containing some combination of "shift", "alt" or "space". Any key not specified is set "up". Use setKeyDown("none") to set all keys in the "up" position. Call setKeyDown("esc") to abort the currently running macro or plugin. For examples, see the CompositeSelections, DoWandDemo and AbortMacroActionTool macros. See also: isKeyDown.
-setLineWidth(width)Specifies the line width (in pixels) used by drawLine(), lineTo(), drawRect() and drawOval().
-setLocation(x, y)Moves the active window to a new location. Use Table.setLocationAndSize(x, y, width, height, title) to set the location and size of a specified window. Use call("ij.gui.ImageWindow.setNextLocation", x, y) to set the location of the next opened window. See also: getLocationAndSize, Table.setLocationAndSize, screenWidth, screenHeight.
-setLocation(x, y, width, height)Moves and resizes the active image window. The new location of the top-left corner is specified by x and y, and the new size by width and height. See also: Table.setLocationAndSize.
-setLut(reds, greens, blues)Creates a new lookup table and assigns it to the current image. Three input arrays are required, each containing 256 intensity values. See the LookupTables macros for examples.
-setMetadata("Info", string)Assigns the metadata in string to the "Info" image property of the current image. This metadata is displayed by Image>Show Info and saved as part of the TIFF header. See also: getMetadata and Property.getInfo.
-setMetadata("Label", string)Sets string as the label of the current image or stack slice. The first 60 characters, or up to the first newline, of the label are displayed as part of the image subtitle. The labels are saved as part of the TIFF header. See also: Property.setSliceLabel and Property.getSliceLabel.
-setMinAndMax(min, max)Sets the minimum and maximum displayed pixel values (display range). See the DisplayRangeMacros for examples.
-setMinAndMax(min, max, channels)Sets the display range of specified channels in an RGB image, where 4=red, 2=green, 1=blue, 6=red+green, etc. Note that the pixel data is altered since RGB images, unlike composite color images, do not have a LUT for each channel.
-setOption(option, boolean)These functions enable or disable ImageJ options, where boolean is either true or false.
-setOption(measurement, boolean)Enable/disables Analyze>Set Measurements options where 'measurement' can be "Display label", "Limit to threshold", "Area", "Mean", "Std", "Perimeter", "Stack position" or "Add to overlay".
-setOption("AntialiasedText", boolean)Controls the "Antialiased text" option in the Edit>Options>Fonts dialog. Requires v1.51h.
-setOption("AutoContrast", boolean)Enables/disables the Edit>Options>Appearance "Auto contrast stacks" option. You can also have newly displayed stack slices contrast enhanced by holding the shift key down when navigating stacks.
-setOption("Bicubic", boolean)Provides a way to force commands like Edit>Selection>Straighten, that normally use bilinear interpolation, to use bicubic interpolation.
-setOption("BlackBackground", boolean)Enables/disables the Process>Binary>Options "Black background" option.
-setOption("Changes", boolean)Sets/resets the 'changes' flag of the current image. Set this option false to avoid "Save Changes?" dialog boxes when closing images.
-setOption("CopyHeaders", boolean)Enables/disables the "Copy column headers" option in the Edit>Options>Input/Output dialog. See String.copyResults Requires v1.52p.
-setOption("DebugMode", boolean)Enables/disables the ImageJ debug mode. ImageJ displays information, such as TIFF tag values, when it is in debug mode.
-setOption("DisablePopupMenu", boolean)Enables/disables the the menu displayed when you right click on an image.
-setOption("DisableUndo", boolean)Enables/disables the Edit>Undo command. Note that a setOption("DisableUndo", true) call without a corresponding setOption("DisableUndo", false) will cause Edit>Undo to not work as expected until ImageJ is restarted.
-setOption("ExpandableArrays", boolean)Enables/disables support for auto-expanding arrays (example).
-setOption("FlipFitsImages", boolean)Controls whether images are flipped vertically by the FITS reader.
-setOption("FullRange16bitInversions", boolean)Set to have 16-bit images inverted using the full range (0-65535). Requires 1.54d.
-setOption("InterpolateLines", boolean)Sets/resets the 'Interpolate line profiles' option in Edit>Options>Plots.
-setOption("InvertY", boolean)Sets/resets the 'invertY' option of the active image.
-setOption("JFileChooser", boolean)Enables/disables use of the Java JFileChooser to open and save files instead of the native OS file chooser.
-setOption("Loop", boolean)Enables/disables the Image>Stacks>Tools>Animation Options "Loop back and forth" option.
-setOption("MonospacedText", boolean)Enables/disables monospaced text in the "Log" window. Requires 1.54c11.
-setOption("OpenUsingPlugins", boolean)Controls whether standard file types (TIFF, JPEG, GIF, etc.) are opened by external plugins or by ImageJ (example).
-setOption("QueueMacros", boolean)Controls whether macros invoked using keyboard shortcuts run sequentially on the event dispatch thread (EDT) or in separate, possibly concurrent, threads (example). In "QueueMacros" mode, screen updates, which also run on the EDT, are delayed until the macro finishes.
-setOption("ScaleConversions", boolean)Enables/disables the "Scale when converting" option in the Edit>Options>Conversions dialog. When this option is enabled (the default), commands in the Image>Type> sub-menu scale from the min and max displayed pixel value to 0-255 when converting from 16-bit or 32-bit to 8-bit or to 0-65535 when converting from 32-bit to 16-bit. The min and max displayed pixel values can be set using the Image>Adjust>Brightness/Contrast dialog or the setMinAndMax() function. Call setOption("CalibrateConversions", true) to have conversions to 8-bit and 16-bit density calibrated. Requires v1.52k.
-setOption("CalibrateConversions", boolean)Enables/disables the "Calibrate conversions" option in the Edit>Options>Conversions dialog. Conversions to 8-bit and 16-bit are density calibrated when this option is enabled, so results from measurements stay the same.
-setOption("Show All", boolean)Enables/disables the the "Show All" mode in the ROI Manager.
-setOption("ShowAngle", boolean)Determines whether or not the "Angle" value is displayed in the Results window when measuring straight line lengths.
-setOption("ShowMin", boolean)Determines whether or not the "Min" value is displayed in the Results window when "Min & Max Gray Value" is enabled in the Analyze>Set Measurements dialog box.
-setOption("WaitForCompletion", boolean)Set false and the next exec() call will return null and not wait for the command being executed to finish. Requires v1.52u.
-setOption("WandAllPoints", boolean)Controls whether Wand selections with straight lines longer than one pixel should have intermediate points with single-pixel spacing. Requires v1.51q.
-setPasteMode(mode)Sets the transfer mode used by the Edit>Paste command, where mode is "Copy", "Blend", "Average", "Difference", "Transparent-white", "Transparent-zero", "AND", "OR", "XOR", "Add", "Subtract", "Multiply", "Divide, "Min" or "Max". The GetCurrentPasteMode macro demonstrates how to get the current paste mode. In ImageJ 1.42 and later, the paste mode is saved and restored by the saveSettings and restoreSettings.
-setPixel(x, y, value)Stores value at location (x, y) of the current image. The screen is updated when the macro exits or call updateDisplay() to have it updated immediately.
-setResult("Column", row, value)Adds an entry to the ImageJ results table or modifies an existing entry. The first argument specifies a column in the table. If the specified column does not exist, it is added. The second argument specifies the row, where 0<=row<=nResults. (nResults is a predefined variable.) A row is added to the table if row=nResults. The third argument is the value to be added or modified. With v1.47o or later, it can be a string. Call setResult("Label", row, string) to set the row label. Call updateResults() to display the updated table in the "Results" window. For examples, see the SineCosineTable and ConvexitySolidarity macros.
-setRGBWeights(redWeight, greenWeight, blueWeight)Sets the weighting factors used by the Analyze>Measure, Image>Type>8-bit and Analyze>Histogram commands when they convert RGB pixels values to grayscale. The sum of the weights must be 1.0. Use (1/3, 1/3, 1/3) for equal weighting of red, green and blue. The weighting factors in effect when the macro started are restored when it terminates. For examples, see the MeasureRGB, ExtractRGBChannels and RGB_Histogram macros.
-setSelectionLocation(x, y)Moves the current selection to (x, y), where x and y are the pixel coordinates of the upper left corner of the selection's bounding rectangle. The RoiManagerMoveSelections macro uses this function to move all the ROI Manager selections a specified distance. See also: getSelectionBounds.
-setSelectionName(name)Sets the name of the current selection to the specified name. Aborts the macro if there is no selection. See also: selectionName and selectionType.
-setSlice(n)Displays the nth slice of the active stack. Does nothing if the active image is not a stack. Use Stack.setPosition(channel, slice, frame) to set hyperstack positions. For an example, see the MeasureStack macros. See also: getSliceNumber, nSlices.
-setThreshold(lower, upper)Sets the lower and upper threshold levels. There is an optional third argument that can be "red", "black & white", "over/under", "no color" or "raw". With density calibrated images, lower and upper must be calibrated values unless the optional third argument is "raw". See also: setAutoThreshold, getThreshold, resetThreshold.
-setTool(name)Switches to the specified tool, where name is "rectangle", "roundrect", "elliptical", "brush", "polygon", "freehand", "line", "polyline", "freeline", "arrow", "angle", "point", "multipoint", "wand", "text", "zoom", "hand" or "dropper". Refer to the SetToolDemo, ToolShortcuts or ToolSwitcher, macros for examples. See also: IJ.getToolName.
-setTool(id)Switches to the specified tool, where 0=rectangle, 1=oval, 2=polygon, 3=freehand, 4=straight line, 5=polyline, 6=freeline, 7=point, 8=wand, 9=text, 10=unused, 11=zoom, 12=hand, 13=dropper, 14=angle, 15...21=custom tools. See also: toolID.
-setupUndo()Call this function before drawing on an image to allow the user the option of later restoring the original image using Edit/Undo. Note that setupUndo() may not work as intended with macros that call the run() function. For an example, see the DrawingTools tool set.
-setVoxelSize(width, height, depth, unit)Defines the voxel dimensions and unit of length ("pixel", "mm", etc.) for the current image or stack. A "um" unit will be converted to "µm". The depth argument is ignored if the current image is not a stack. See also: getVoxelSize.
-setZCoordinate(z)Sets the Z coordinate used by getPixel(), setPixel() and changeValues(). The argument must be in the range 0 to n-1, where n is the number of images in the stack. For an examples, see the Z Profile Plotter Tool.
-showMessage("message")Displays "message" in a dialog box. Can display HTML formatted text (example).
-showMessage("title", "message")Displays "message" in a dialog box using "title" as the the dialog box title. Can display HTML formatted text (example).
-showMessageWithCancel(["title", ]"message")Displays "message" in a dialog box with "OK" and "Cancel" buttons. "Title" (optional) is the dialog box title. The macro exits if the user clicks "Cancel" button. See also: getBoolean.
-showProgress(progress)Updates the ImageJ progress bar, where 0.0<=progress<=1.0. The progress bar is not displayed if the time between the first and second calls to this function is less than 30 milliseconds. It is erased when the macro terminates or progress is >=1.0. Use negative values to show subordinate progress bars as moving dots (example).
-showProgress(currentIndex, finalIndex)Updates the progress bar, where the length of the bar is set to currentIndex/finalIndex of the maximum bar length. The bar is erased if currentIndex>finalIndex or finalIndex==0.
-showStatus("message")Displays a message in the ImageJ status bar. If message starts with '!', subsequent process messages are suppressed (example).
-showText("string")Displays a string in a text window.
-showText("Title", "string")Displays a string in a text window using the specified title.
-sin(angle)Returns the sine of an angle (in radians).
-snapshot()Creates a backup copy of the current image that can be later restored using the reset function. For examples, see the ImageRotator and BouncingBar macros.
-split(string, delimiters)Breaks a string into an array of substrings. Delimiters is a string containing one or more delimiter characters. The default delimiter set " \t\n\r" (space, tab, newline, return) is used if delimiters is an empty string or split is called with only one argument. Multiple delimiters in the string are merged (taken as one) and delimiters at the start or end of the string are ignored unless the delimiter is a single comma, a single semicolon or a regular expression. With ImageJ 1.49f or later, delimiters can be also a regular expression enclosed in parentheses, e.g. delimiters="(\n\n)" splits only at empty lines (two newline characters following each other). See also: String.join.
-Note that split() may return empty strings when the second argument is ",", ";' or "\n". To avoid empty strings, use ",,", ";;" and "\n\n" as the second argument.
-sqrt(n)Returns the square root of n. Returns NaN if n is less than zero.
-Stack (hyperstack) These functions allow you to get and set the position (channel, slice and frame) of a hyperstack (a 4D or 5D stack). The HyperStackDemo demonstrates how to create a hyperstack and how to work with it using these functions
-Stack.isHyperstackReturns true if the current image is a hyperstack.
-Stack.getDimensions(width, height, channels, slices, frames) Returns the dimensions of the current image.
-Stack.setDimensions(channels, slices, frames)Sets the 3rd, 4th and 5th dimensions of the current stack.
-Stack.setChannel(n)Displays channel n .
-Stack.setSlice(n)Displays slice n .
-Stack.setFrame(n)Displays frame n .
-Stack.getPosition(channel, slice, frame)Returns the current position.
-Stack.setPosition(channel, slice, frame)Displays the specified channel, slice and frame.
-Stack.getFrameRate()Returns the frame rate (FPS).
-Stack.setFrameRate(fps)Sets the frame rate.
-Stack.getFrameInterval()Returns the frame interval in time (T) units.
-Stack.setFrameInterval(interval)Sets the frame interval in time (T) units.
-Stack.getUnits(X, Y, Z, Time, Value)Returns the x, y, z, time and value units.
-Stack.setUnits(X, Y, Z, Time, Value)Sets the x, y, z, time and value units.
-Stack.setXUnit(string)Sets the X-dimension unit.
-Stack.setYUnit(string)Sets the Y-dimension unit.
-Stack.setZUnit(string)Sets the Z-dimension unit.
-Stack.setTUnit(string)Sets the time unit.
-Stack.setDisplayMode(mode)Sets the display mode, where mode is "composite", "color" or "grayscale". Requires a multi-channel stack.
-Stack.getDisplayMode(mode)Sets the string mode to the current display mode.
-Stack.setActiveChannels(string)Controls which channels in a composite color image are displayed, where string is a list of ones and zeros that specify the channels to display. For example, "101" causes channels 1 and 3 to be displayed.
-Stack.getActiveChannels(string)Returns a string that represents the state of the channels in a composite color image, where '1' indicates a displayed channel and '0' indicates an inactive channel.
-Stack.toggleChannel(channel)Switches the display state of the specified channel of a composite color image.
-Stack.swap(n1, n2)Swaps the two specified stack images, where n1 and n2 are integers greater than 0 and less than or equal to nSlices.
-Stack.getStatistics(voxelCount, mean, min, max, stdDev)Calculates and returns stack statistics.
-Stack.setOrthoViews(x, y, z)If an Orthogonal Views is active, its crosspoint is set to x, y, z (example).
-Stack.getOrthoViews(x, y, z)If an Orthogonal Views is active, its crosspoint is returned as x, y, z values.
-Stack.getOrthoViewsIDReturns the image ID of the current Orthogonal Views, or zero if none is active.
-Stack.getOrthoViewsIDs(XY, YZ, XZ)If an Orthogonal Views is active, the three views are returned as XY, YZ, XZ image ID values.
-Stack.stopOrthoViewsStops the current Orthogonal Views and closes the "YZ" and "XZ" windows.
-startsWith(string, prefix) Returns true (1) if string starts with prefix. See also: endsWith, indexOf, substring, toLowerCase, matches.
-charAt(i)
-contains(s2)
-endsWith(s2)
-indexOf(s2)
-lastIndexOf(s2)
-length
-matches(s2)
-replace(s1, s2)
-startsWith(s2)
-substring(i1, i2)
-substring(i)
-toLowerCase
-toUpperCase
-trim
-String.resetBufferResets (clears) the buffer.
-String.append(str)Appends str to the buffer.
-String.bufferReturns the contents of the buffer.
-String.copy(str)Copies str to the clipboard.
-String.copyResultsCopies the Results table, or selected rows in the Results table, to the clipboard. Column headers are included if the "Copy column headers" option in the Edit>Options>Input/Output dialog is enabled. Use SetOption("CopyHeaders", boolean) to programmatically enable/disable this option.
-String.getResultsHeadingsReturns the Results window headers. Example.
-String.format(format, n1, n2, ...)Returns a formatted string using the specified format and numbers.
-String.pad(n, length)Pads 'n' with leading zeros so that it is 'length' characters wide and returns the result. Note that 'n' can be either a number or a string. For an example, run the Help>Examples>Macro>Stack Overlay command.
-String.pasteReturns the contents of the clipboard.
-String.join(array)Creates a ", " delimited string from the elements of 'array'. See also: split.
-String.join(array, delimiter)Creates a string from the elements of 'array', using the specified string delimiter.
-String.trim(string)Returns a copy of 'string' that has leading and trailing whitespace omitted. Can be replaced with string.trim() in ImageJ 1.52t and later.
-String.show(str)Displays str in a text window.
-String.show(title, str)Displays str in a text window using title as the title.
-String.setFontSize(size)Sets the size of the font used by drawString(). Requires 1.53v.
-substring(string, index1, index2)Returns a new string that is a substring of string. The substring begins at index1 and extends to the character at index21. Can be replaced with str.substring(i1, i2) in ImageJ 1.52t and later. See also: indexOf, startsWith, endsWith, replace.
-substring(string, index)Returns a substring of string that begins at index and extends to the end of string. Can be replaced with str.substring(i) in ImageJ 1.52t and later.
-Table.create(name)Creates or resets a table. If the table exists, it is reset (cleared), otherwise a new table with the specified name is opened.
-Table.reset(name)Resets the specified table.
-Table.sizeThe number of rows in the current table.
-Table.titleThe title (name) of the current table.
-Table.headingsThe column headings as a tab-delimited string.
-Table.allHeadingsAll 38 default measument headings as a tab-delimited string.
-Table.get(columnName, rowIndex)Returns the numeric value from the cell at the specified column and row.
-Table.getString(columnName, rowIndex)Returns a string value from the cell at the specified column and row.
-Table.set(columnName, rowIndex, value)Assigns a numeric or string value to the cell at the specified column and row.
-Table.getColumn(columnName)Returns the specified column as an array.
-Table.setColumn(columnName, array)Assigns an array to the specified column, where 'array' can contain either numbers and/or strings. A new column is added to the table if 'columnName' does not exist.
-Table.renameColumn(oldName, newName)Renames a column.
-Table.deleteColumn(columnName)Deletes the specified column.
-Table.columnExists(columnName)Returns 'true' if the specified column exists. Requires 1.53p.
-Table.updateUpdates the window displaying the current table.
-Table.rename(oldName, newName)Renames a table.
-Table.setSelection(firstRowIndex, lastRowIndex)Selects a range of rows in the current table. Use range (-1, -1) for selecting none.
-Table.getSelectionStartReturns the index of the first selected row in the current table, or1 if there is no selection.
-Table.getSelectionEndReturns the index of the last selected row in the current table, or -1 if there is no selection.
-Table.save(filePath)Saves a table.
-Table.open(filePath)Opens a table.
-Table.deleteRows(firstIndex, lastIndex)Deletes specified rows.
-Table.sort(column)Sorts the table on the specified column (example).
-Table.showRowNumbers(boolean)Enable/disable display of row numbers. Default is 'false'. Does not work with the standard "Results" table, which always has row numbers.
-Table.showRowIndexes(boolean)Enable/disable display of row indexes.
-Table.saveColumnHeader(boolean)The column header row is not saved if the argument is 'false' (default is 'true').
-Table.showArrays(title, array1, array2, ...)Displays arrays in a table (same as Array.show). If title ends with "(indexes)", a 0-based Index column is shown. If it ends with "(row numbers)", the row number column is shown.
-Table.applyMacro(code)Applies macro code to each row of the table. Columns are assigned variable names as given by Table.headings. For columns (%Area, Perim. and Circ.), special characters are replaced by underscores (_Area, Perim_ and Circ_). New variables starting with an uppercase letter create a new column with this name. The variable 'row' (row index) is pre-defined. Currently only supports numeric values except for row labels.
-Table.setLocationAndSize(x, y, width, height)Sets the location and size of the current table. Works with other types of windows if a title is specified as the fifth argument.
-tan(angle)Returns the tangent of an angle (in radians).
-toBinary(number)Returns a binary string representation of number. Use IJ.pad to add leading zeros.
-toHex(number)Returns a hexadecimal string representation of number. Use IJ.pad to add leading zeros.
-toLowerCase(string)Returns a new string that is a copy of string with all the characters converted to lower case.
-toolID Returns the ID of the currently selected tool. See also: setTool, IJ.getToolName.
-toScaled(x, y)Converts unscaled pixel coordinates to scaled coordinates using the properties of the current image or plot. Also accepts arrays.
-toScaled(x, y, z)Converts unscaled (x, y, z) pixel coordinates to scaled coordinates.
-toUnscaled(x, y)Converts scaled coordinates to unscaled pixel coordinates using the properties of the current image or plot. Also accepts arrays. Refer to the AdvancedPlots macro set for examples.
-toUnscaled(x, y, z)Converts scaled (x, y, z) pixel coordinates to unscaled (raw) coordinates.
-toScaled(length)Converts (in place) a horizontal length in pixels to a scaled length using the properties of the current image. In a plot with Log scale, the scaled value is regarded as an exponent of 10.
-toUnscaled(length)Converts (in place) a scaled horizontal length to a length in pixels using the properties of the current image. In a plot with Log scale, the scaled value is regarded as an exponent of 10.
-toString(number)Returns a decimal string representation of number. See also: toBinary, toHex, parseFloat and parseInt.
-toString(number, decimalPlaces)Converts number into a string, using the specified number of decimal places. See also: d2s.
-toUpperCase(string)Returns a new string that is a copy of string with all the characters converted to upper case.
-updateDisplay()Redraws the active image.
-updateResults()Call this function to update the "Results" window after the results table has been modified by calls to the setResult() function.
-wait(n)Delays (sleeps) for n milliseconds.
-waitForUser(string)Halts the macro and displays string in a dialog box. The macro proceeds when the user clicks "OK" or it is aborted if the user clicks on "Cancel". Unlike showMessage, the dialog box is not modal, so the user can, for example, create a selection or adjust the threshold while the dialog is open. To display a multi-line message, add newline characters ("\n") to string. This function is based on Michael Schmid's Wait_For_User plugin. Example: WaitForUserDemo.
-waitForUser(title, message)This is a two argument version of waitForUser, where title is the dialog box title and message is the text displayed in the dialog.
-waitForUser This is a no argument version of waitForUser that displays "Click OK to continue" in the dialog box.
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