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'''Image selection using the GenericDialog class
This code is part of the Jython tutorial at the ImageJ wiki.
http://imagej.net/Jython_Scripting#Image_selection_using_the_GenericDialog_class
'''
# The module __future__ contains some useful functions:
# https://docs.python.org/2/library/__future__.html
from __future__ import with_statement, division
# This imports the function random from the module random.
from random import random
# Next we import Java Classes into Jython.
# This is how we can acces the ImageJ API:
# https://imagej.nih.gov/ij/developer/api/allclasses-noframe.html
from ij import IJ, WindowManager
from ij.gui import GenericDialog
# A function is created with the def keyword.
# This function does not need any parameters.
def create_test_image():
# Python uses indentation to create code blocks
# Local variables are assigned.
# We can assign the same value to more than one variable.
image_width = image_height = 512
box_width = box_height = 128
offset_x = offset_y = 192
counts = 64
stdv = 16
# The build in function int() is used to convert float to int.
# The variable random contains a function that is called by adding parentheses.
offset_x = int(2 * random() * offset_x)
offset_y = int(2 * random() * offset_y)
# We can define a function inside a function.
# Outside of create_test_image() this function is not available.
# By adding an asterisk to a parameter, all given parameters are combined to a tuple.
def make_title(*to_concat):
prefix = 'TestImage'
# To create a tuple with a single entry the comma is necessary.
# The 2 tuples are concatenated by using the + operator.
to_join = (prefix,) + to_concat
# We create a generator that converts every singe entry of the tuple to a string.
strings_to_join = (str(arg) for arg in to_join)
# The string ',' has a join method to concatenate values of a tuple with the string as seperator.
# The result is a string.
return ','.join(strings_to_join)
def check_existence(title):
if WindowManager.getIDList() is None:
return False
image_titles = (WindowManager.getImage(id).getTitle() for id in WindowManager.getIDList())
return title in image_titles
# To negate an expression put not in front of it.
if not check_existence(make_title(offset_x, offset_y)):
# The following code has been created by using the Recorder of ImageJ, set to output Java code.
# By removing the semicolons, the code can be used in Jython.
# The parameters can be modified by using variables and string concatenation.
imp = IJ.createImage(make_title(offset_x, offset_y), "8-bit black", image_width, image_height, 1)
# The build in function str() is used to convert int to string.
IJ.run(imp, "Add...", "value=" + str(counts))
imp.setRoi(offset_x , offset_y, box_width, box_height)
IJ.run(imp, "Add...", "value=" + str(counts))
IJ.run(imp, "Select None", "")
IJ.run(imp, "Add Specified Noise...", "standard=" + str(stdv));
# We don't want to confirm when closing one of the newly created images.
imp.changes = False
imp.show()
# This function uses parameters.
# A default value is given to the third parameter.
def create_selection_dialog(image_titles, defaults, title='Select images for processing'):
gd = GenericDialog(title)
# The build in function enumerate() returns two values:
# The index and the value stored in the tuple/list.
for index, default in enumerate(defaults):
# for each loop we add a new choice element to the dialog.
gd.addChoice('Image_'+ str(index + 1), image_titles, image_titles[default])
gd.showDialog()
if gd.wasCanceled():
return None
# This function returns a list.
# _ is used as a placeholder for values we don't use.
# The for loop is used to call gd.getNextChoiceIndex() len(defaults) times.
return [gd.getNextChoiceIndex() for _ in defaults]
# It's best practice to create a function that contains the code that is executed when running the script.
# This enables us to stop the script by just calling return.
def run_script():
while WindowManager.getImageCount() < 10:
create_test_image()
image_titles = [WindowManager.getImage(id).getTitle() for id in WindowManager.getIDList()]
# range(3) will create the list [0, 1, 2].
selected_indices = create_selection_dialog(image_titles, range(3))
# The script stops if the dialog has ben canceld (None was returned from create_selection_dialog).
if selected_indices is None:
print('Script was canceld.')
return
# We have to get the corresponding IMagePlus objects.
selected_imps = [WindowManager.getImage(id) for id in [WindowManager.getIDList()[index] for index in selected_indices]]
# The previous line can be split into 2 lines:
# selected_ids = [WindowManager.getIDList()[index] for index in selected_indices]
# selected_imps = [WindowManager.getImage(id) for id in selected_ids]
for imp in selected_imps:
# Strings can be formated using the % operator:
# http://www.learnpython.org/en/String_Formatting
IJ.log('The image \'%s\' has been selected.' % imp.getTitle())
# If a Jython script is run, the variable __name__ contains the string '__main__'.
# If a script is loaded as module, __name__ has a different value.
if __name__ in ['__builtin__','__main__']:
run_script()
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