imagey - ImageJ with CPython REPL

NOTE: Currently, legacy-imglib1-1.1.8.jar cannot be on class path (see #3). This should make it work:

mv /path/to/Fiji.app/jars/legacy-imglib1-<VERSION>.jar{.bkp,}

This uses ImageJ2 because shared memory would not be possible with ImageJ1 ImageProcessor data structures.

Dependencies

• imglyb
  • Follow build instructions, or
  • install from conda: conda install -c hanslovsky imglib2-imglyb
• PyQt5
  • Install through your package manager, or
  • pip install pyqt5
• QtConsole
  • Install through your package manager, or
  • pip install qtconsole
• Fiji
  • Download Fiji and run Update...
  • Add (http://sites.imagej.net/Hanslovsky/) to update sites and update scifio.jar.

Run

python /path/to/imagey/imagey/imagey.py [-j '<java options>'] /path/to/Fiji.app

Switch to modern mode:

Help>Switch to Modern Mode

To start the CPython repl, navigate the Fiji menu to

Plugins>Scripting>CPython REPL

For conevenience, these variables are exposed to the IPython interpretor:

Variable	Description
ij	ImageJ instance
factory	ImgFactory instance for numpy convertibale Img
opener	ImgOpener instance
display	DisplayService used by active ImageJ instance
open_imgs	Open all images at path through ImgOpener
open_img	Open image at path through ImgOpener
show_img	Show image (numpy or imglib2) through DisplayService used by active ImageJ instance
imglyb	imglib2-imglyb module
util	imglyb.util
types	imglyb.types
np	numpy package
autoclass	jnius.autoclass
cast	jnius.cast
java_method	jnius.java_method
PythonJavaClass	jnius.PythonJavaClass
jnius_config	config module for jnius

These keyboard shortcuts are available:

Shortcut	Action
C-+	Increase font size
C--	Decrease font size
C-0	Reset font size
C-p	Reload initial variables