A 3D editing plugin

• 2003 Open as stack
• 2003 BioRad Reader Multi
• 2003 Duplicate image
• 2003 JNI ColorProcessor
• 2003 Montage Assistant
• 2004 Open image and notes
• 2005-01-25 Smaller
• 2004 QuickIJ
• 2005-02-02 CLI
• 2005-09-22 PostgreSQL
• 2005-10-20 Open sequentially as a stack
• 2005-10-28 Jython utilities
• 2005-10-30 Benchmark comparison between java plugins, macros and jython scripts
• 2005-11-01 Jython interpreter for ImageJ
• 2005-11-11 PDF Viewer: open a PDF file as a stack.
• 2005-12-17 Image Browser: browse images, stacks and image sequences within the same window.

• open c:/Folder/Images/baboon.jpg
• open("baboon.jpg")        (on folder c:/Folder/Images )
• open baboon*
• open *boon.jpg
• open *boon*

• doCommand("Invert");
• makeRectangle(10,10,100,200);

• dc invert
• makeRectangle 10,10,100,200

macro "AutoRun" { run("Refresh Jython List"); }

• Add_Noise.java: 1-2 s
• Add_Noise.txt: 12 s
• Add_Noise_1.py: 15 s (pythonesque version using java.util.Random)
• Add_Noise.py: 44 s (macro-like version, but using python's random.randint() function)

>>> img = Windowmanager.getCurrentImage()
>>> def toStack(image):
...    stack = ImageStack(image.width, image.height)
...    for i in range(10):
...        stack.addSlice(image.getTitle(), image.getProcessor().crop())
...    
...    ImagePlus("stack", stack).show()
...
>>> toStack(img)

>>> from java.awt import FileDialog
>>> fd = FileDialog(IJ.getInstance(), "Open", FileDialog.LOAD)
>>> fd.show()
>>> file_name = fd.getFile()
>>> if None != file_name:
...    Opener().openImage(fd.getDirectory, file_name).show()
...
>>>

>>> IJ.run("Select All")
None
>>> IJ.doCommand("Select All")
None

>>> IJ.runMacro("showMessage(\"called from a macro\");")

>>> c = WindowManager.getCurrentImage
>>> img = c()
>>> print img
imp[test_8-bit.tif 600x900x1]
>>>

>>> from java.io import File, FilenameFilter
>>> import re
>>> class Filter(FilenameFilter):
...	def accept(self, dir, name):
...		reg = re.compile("\.tif$")
...		m = reg.search(name)
...		if m:
...			return 1
...		else:
...			return 0
...
>>>
>>> folder = "/images/art/"
>>> tifs = [Opener().openImage(folder, file.name) for file in File(folder).listFiles(Filter())]
>>> print tifs
[imp[image1.tif 600x900x1], imp[image2.tif 600x900x1], imp[image3.tif 600x900x1]]

>>> class Stack(ImageStack):
...	def __init__(self, title, imp):
...		ImageStack.__init__(self, imp.width, imp.height)
...		self.title = title
...		self.addSlice(imp.title, imp.getProcessor())
...		
...	def __add__(self, imp):
...		if imp.width == self.width and imp.height == self.height:
...			self.addSlice(imp.title, imp.getProcessor())
...		else:
...			print "image", imp.getTitle(), "has different dimensions. Ignoring."
...		return self
...
...	def show(self):
...		ImagePlus(self.title, self).show()
...
>>>
>>> img = WindowManager.getCurrentImage()
>>> stack = Stack("stack", img) + img + img + img
>>> stack.show()

>>> w = WindowManager
>>> stack = None
>>> for id in w.getIDList():
...	img = w.getImage(id)
...	if None == stack: stack = Stack("all", img)
...	else: stack += img
...
>>>
>>> stack.show()

$ cd /Applications/ImageJ/plugins/Jython/
$ /Applications/ImageJ/jython-2.1/jythonc -J "-classpath \
/Applications/ImageJ/ImageJ.app/Contents/Resources/Java/ij.jar" -w . Add_Noise_1.py

>>> from javax.swing import JFrame
>>> from java.awt import Color, Dimension
>>> f = JFrame("Test", size=Dimension(400,400), \
...	windowClosing=lambda msg: IJ.showMessage("Closing the window!"), \
...	visible=1, background=Color.yellow)
...
>>>
>>> img = WindowManager.getCurrentImage()
>>> ic = img.getWindow().getCanvas()
>>> f.getContentPane().add(ic)

>>> def closing(an_event):
... 	IJ.showMessage("Closing!")
...
>>>
>>> f = JFrame("Test", visible=1, windowClosing=closing)

• Jython.org: download Jython, read documentation.
• Jython in ImageJ tutorial by Edoardo Marcora.
• jython specs and examples

• Click to select. The title changes to show the selected image.
• Use '<' and '>' keys to navigate the stack or sequence, or drag the scroll bar.
• Navigate with the glass (zoom) and hand tools. Also zoom with the '+' and '-' keys.
• Double-click to open in a separate window (with any tool but the glass).
• Shift double-click to release all resources, except for what shows (as awt.Image objects), so that images can be zoomed and panned using a minimal ammount of memory (with any tool but the glass).