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.

In [1]:

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: 2.9.0/1.53t
Legacy layer active: True

In [2]:

# 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.