Examples of how to use imageJ macros

imageJ_ScriptParameters

Here are some simple examples on how to use script parameters to simplify input for imageJ macros

Example script parameters

#@ String (visibility=MESSAGE, value="PERSONAL INFO") msg1
#@ String (label = "Your name")  name
#@ Date (label = "Date of birth") dob
#@ ColorRGB (label = "Favorite color", default = "255,0,204") rgb
#@ String (visibility=MESSAGE, value="PROGRAMMING SKILLS") msg2
#@ Integer(label = "Programming experience", min = 1, max = 10, style = "slider") prog_exp
#@ Boolean (label = "Process subfolders") subfolders
#@ String (visibility=MESSAGE, value="OUTPUT") msg3
#@ File (label="Select a directory", style="directory") myDir

Hello world

You can write imageJ macros in any of the script languages with parameters to define input and output.

Hello imageJ

#@ String(label = "Your name") name
#@ OUTPUT String greeting

## Hello ImageJ 
greeting = "Hello, " + str(name) + "!"
#print(greeting)

If you save this scirpt in the plugins folder .../Fiji.app/plugins/ you can call your script using the imageJ GUI or using the run function in your macros

Call Hello ImageJpy

from ij import IJ

#A test dataset
test_data = ["person 1", "person 2", "person 3", "person 4"]

# make greetings 
for name in test_data:
	IJ.run("Hello imageJ py", "name=[" + name + "]")

Import your own modules

Save usefull functions in modules that you can import from other imageJ macros. based on self-written-jython-modules-for-imagej

• Make a folder in the .../Fiji.app/jars/ folder called Lib.
• save your macro containing your functions there

hello_imageJ_module

def helloImageJ(name):
	print "hello", name

def helloImageJ_upper(name):
	print "hello", (name.upper())

• restart imageJ
• import your module to a new script

call_hello_imageJ_module

import hello_imageJ_module as him
# hello_imageJ_module.py must be saved in `.../Fiji.app/jars/Lib/` folder

# List all possible functions
print dir(him)

# You can run your function like this
him.helloImageJ("normic")
him.helloImageJ_upper("normic")

if you only need one function from your module you can import only that

from hello_imageJ_module import helloImageJ
helloImageJ("normic")