def fn_launch_frame(event):
javabridge.execute_runnable_in_main_thread(javabridge.run_script("""
new java.lang.Runnable() {
run: function() {
with(JavaImporter(java.awt.Frame)) Frame().setVisible(true);
}
};"""))
def finalize(self, result):
try:
javabridge.deactivate_awt()
import imagej.imagej2
if imagej.imagej2.the_imagej_context is not None:
script = """
new java.lang.Runnable () {
run: function() {
ctx.getContext().dispose();
}
}"""
runnable = javabridge.run_script(
script, dict(ctx=imagej.imagej2.the_imagej_context))
javabridge.execute_runnable_in_main_thread(runnable, True)
imagej.imagej2.the_imagej_context = None
javabridge.static_call("java/lang/System", "gc", "()V")
except:
pass
try:
from ilastik.core.jobMachine import GLOBAL_WM
GLOBAL_WM.stopWorkers()
except:
logging.root.warn("Failed to stop Ilastik")
try:
from cellprofiler.utilities.zmqrequest import join_to_the_boundary
join_to_the_boundary()
except:
logging.root.warn("Failed to stop zmq boundary")
def fn_launch_frame(event):
javabridge.execute_runnable_in_main_thread(
javabridge.run_script("""
new java.lang.Runnable() {
run: function() {
with(JavaImporter(java.awt.Frame)) Frame().setVisible(true);
}
};"""))
def setActiveDisplay(self, display):
'''Make this the active display'''
# Note: has to be run in GUI thread on mac
r = J.run_script(
"""new java.lang.Runnable() {
run:function() { displayService.setActiveDisplay(display); }
}
""", dict(displayService=self.o, display=display.o))
J.execute_runnable_in_main_thread(r, True)
def setActiveDisplay(self, display):
'''Make this the active display'''
# Note: has to be run in GUI thread on mac
r = J.run_script(
"""new java.lang.Runnable() {
run:function() { displayService.setActiveDisplay(display); }
}
""", dict(displayService=self.o, display=display.o))
J.execute_runnable_in_main_thread(r, True)
def hide(self):
J.execute_runnable_in_main_thread(
J.run_script(
"""
new java.lang.Runnable() {
run: function() { o.hide(); }}""",
dict(o=self.o),
),
synchronous=True,
)
def set_temp_current_image(imagej_obj):
'''Set the temporary current image for the UI thread'''
script = """
new java.lang.Runnable() {
run: function() {
Packages.ij.WindowManager.setTempCurrentImage(ip);
}
};
"""
javabridge.execute_runnable_in_main_thread(
javabridge.run_script(script, dict(ip=imagej_obj.o)), True)
def execute_macro(macro_text):
'''Execute a macro in ImageJ
macro_text - the macro program to be run
'''
interp = J.make_instance("ij/macro/Interpreter","()V");
J.execute_runnable_in_main_thread(J.run_script(
"""new java.lang.Runnable() {
run: function() {
interp.run(macro_text);
}}""", dict(interp=interp, macro_text=macro_text)), synchronous=True)
def close(self):
'''Close the display
This is run in the UI thread with synchronization.
'''
r = J.run_script(
"""new java.lang.Runnable() {
run: function() { display.close(); }
};
""", dict(display=self.o))
J.execute_runnable_in_main_thread(r, True)
def execute_macro(macro_text):
'''Execute a macro in ImageJ
macro_text - the macro program to be run
'''
interp = javabridge.make_instance("ij/macro/Interpreter", "()V");
javabridge.execute_runnable_in_main_thread(javabridge.run_script(
"""new java.lang.Runnable() {
run: function() {
interp.run(macro_text);
}}""", dict(interp=interp, macro_text=macro_text)), synchronous=True)
def close(self):
'''Close the display
This is run in the UI thread with synchronization.
'''
r = J.run_script(
"""new java.lang.Runnable() {
run: function() { display.close(); }
};
""", dict(display=self.o))
J.execute_runnable_in_main_thread(r, True)
def set_temp_current_image(imagej_obj):
'''Set the temporary current image for the UI thread'''
script = """
new java.lang.Runnable() {
run: function() {
Packages.ij.WindowManager.setTempCurrentImage(ip);
}
};
"""
J.execute_runnable_in_main_thread(
J.run_script(script, dict(ip=imagej_obj.o)), True)
def select_overlay(display, overlay, select=True):
'''Select or deselect an overlay
display - the overlay's display
overlay - the overlay to select
'''
for view in J.get_collection_wrapper(display, fn_wrapper = wrap_data_view):
if J.call(overlay, "equals", "(Ljava/lang/Object;)Z", view.getData()):
J.execute_runnable_in_main_thread(J.run_script(
"""new java.lang.Runnable() {
run: function() { view.setSelected(select);}
}""", dict(view = view.o, select=select)), synchronous=True)
break
else:
logger.info("Failed to select overlay")
def select_overlay(display, overlay, select=True):
'''Select or deselect an overlay
display - the overlay's display
overlay - the overlay to select
'''
for view in J.get_collection_wrapper(display, fn_wrapper = wrap_data_view):
if J.call(overlay, "equals", "(Ljava/lang/Object;)Z", view.getData()):
J.execute_runnable_in_main_thread(J.run_script(
"""new java.lang.Runnable() {
run: function() { view.setSelected(select);}
}""", dict(view = view.o, select=select)), synchronous=True)
break
else:
logger.info("Failed to select overlay")
def set_current_image(imagej_obj):
'''Set the currently active window
imagej_obj - an ImagePlus to become the current image
'''
javabridge.execute_runnable_in_main_thread(javabridge.run_script(
"""new java.lang.Runnable() {
run:function() {
var w = imp.getWindow();
if (w == null) {
imp.show();
} else {
Packages.ij.WindowManager.setCurrentWindow(w);
}
}
}
""", dict(imp=imagej_obj.o)), synchronous=True)
def set_current_image(imagej_obj):
'''Set the currently active window
imagej_obj - an ImagePlus to become the current image
'''
J.execute_runnable_in_main_thread(J.run_script(
"""new java.lang.Runnable() {
run:function() {
var w = imp.getWindow();
if (w == null) {
imp.show();
} else {
Packages.ij.WindowManager.setCurrentWindow(w);
}
}
}
""", dict(imp=imagej_obj.o)),
synchronous=True)
def test_06_02_execute_synch_main(self):
javabridge.execute_runnable_in_main_thread(javabridge.run_script(
"new java.lang.Runnable() { run:function() {}};"), True)
def show(self):
javabridge.execute_runnable_in_main_thread(javabridge.run_script("""
new java.lang.Runnable() {
run: function() { o.show(); }}""", dict(o=self.o)),
synchronous=True)
def test_06_02_execute_synch_main(self):
javabridge.execute_runnable_in_main_thread(
javabridge.run_script(
"new java.lang.Runnable() { run:function() {}};"), True)
def hide(self):
javabridge.execute_runnable_in_main_thread(javabridge.run_script(
"""
new java.lang.Runnable() {
run: function() { o.hide(); }}""", dict(o=self.o)),
synchronous=True)
