This notebook is part of the PyImageJ Tutorial Series, and assumes familiarity with the ImageJ API. Dedicated tutorials for ImageJ can be found here.

5 Convenience methods of PyImageJ

PyImageJ is built to provide easy access to key ImageJ resources. We call these collective methods “convenience methods”. These methods are attached toij.py after initializing ImageJ. Here’s a quick list of some of the more useful methods and additional information.

`ij.py.`	function	more information
`show`	Show an image	06-Working-with-Images
`to_java`	Convert data from Python to Java	03-Sending-Data-to-Java
`from_java`	Convert data from Java to Python	04-Retrieving-Data-from-Java
`run_macro`	Run an original ImageJ macro	07-Running-Macros-Scripts-and-Plugins
`run_script`	Run an ImageJ script (supported languages)	07-Running-Macros-Scripts-and-Plugins
`run_plugin`	Run a plugin	07-Running-Macros-Scripts-and-Plugins
`initialize_numpy_image`	Create a new numpy image in the same shape as input image	06-Working-with-Images
`sync_image`	Synchronize data between ImageJ and ImageJ2 data structures	–
`active_dataset`	Get the active image as a `Dataset`	–
`active_xarray`	Get a copy of the active image as an `xarray.DataArray`	–
`active_imageplus`	Get the `ImagePlus` from the current window	–

There are other convenience methods that are attached to ij.py. After initializing ImageJ you can explore ij.py’s methods with dir.

5.1 Other convenient access to ImageJ functions

When the original ImageJ is available (i.e. the legacy layer is active) IJ, WindowManager, ResultsTable and RoiManager are accessible directly from the initialized ij object.

import imagej

# initialize imagej
ij = imagej.init()
print(f"ImageJ2 version: {ij.getVersion()}")

# first check if the legacy layer is active
print(f"Legacy layer active: {ij.legacy.isActive()}")

Operating in headless mode - the original ImageJ will have limited functionality.

ImageJ2 version: 2.14.0/1.54f
Legacy layer active: True

# demonstrate access to classes
print(ij.IJ)
print(ij.ResultsTable)
print(ij.RoiManager)
print(ij.WindowManager)

Operating in headless mode - the IJ class will not be fully functional.
Operating in headless mode - the ResultsTable class will not be fully functional.
Operating in headless mode - the RoiManager class will not be fully functional.
Operating in headless mode - the WindowManager class will not be fully functional.

<java class 'ij.IJ'>
<java class 'ij.measure.ResultsTable'>
<java class 'ij.plugin.frame.RoiManager'>
<java class 'ij.WindowManager'>

Note the warnings! We’re currently in headless mode. The many legacy ImageJ functions operate limitedly or not at all in headless mode. For example the RoiManager is not functional in a true headless enviornment.