def test_05_07_get_pixel_data_3d(self):
svc = ij2.get_dataset_service(self.context)
result = svc.create1(np.array([10, 7, 3]),
"MyDataset",
[ij2.Axes().Y, ij2.Axes().X, ij2.Axes().CHANNEL],
16, False, False)
imgplus = result.getImgPlus()
script = """
ra = imgplus.randomAccess();
for (x=0;x<imgplus.dimension(0);x++) {
ra.setPosition(x, 0);
for (y=0;y<imgplus.dimension(1);y++) {
ra.setPosition(y, 1);
for (c=0;c<imgplus.dimension(2);c++) {
ra.setPosition(c, 2);
ra.get().set(x + y * 10 + c * 100);
}
}
}
"""
J.run_script(script, dict(imgplus=imgplus))
pixel_data = ij2.get_pixel_data(imgplus)
self.assertSequenceEqual(pixel_data.shape, [10, 7, 3])
i, j, c = np.mgrid[0:10, 0:7, 0:3]
np.testing.assert_array_equal(pixel_data, i + j*10 + c*100)
def write_image(pathname, pixels, pixel_type, c=0, z=0, t=0, size_c=1, size_z=1, size_t=1, channel_names=None):
"""Write the image using bioformats
filename - save to this filename
pixels - the image to save
pixel_type - save using this pixel type
c - the image's channel index
z - the image's z index
t - the image's t index
sizeC - # of channels in the stack
sizeZ - # of z stacks
sizeT - # of timepoints in the stack
channel_names - names of the channels (make up names if not present
"""
omexml = ome.OMEXML()
omexml.image(0).Name = os.path.split(pathname)[1]
p = omexml.image(0).Pixels
assert isinstance(p, ome.OMEXML.Pixels)
p.SizeX = pixels.shape[1]
p.SizeY = pixels.shape[0]
p.SizeC = size_c
p.SizeT = size_t
p.SizeZ = size_z
p.DimensionOrder = ome.DO_XYCZT
p.PixelType = pixel_type
index = c + size_c * z + size_c * size_z * t
if pixels.ndim == 3:
p.SizeC = pixels.shape[2]
p.Channel(0).SamplesPerPixel = pixels.shape[2]
omexml.structured_annotations.add_original_metadata(ome.OM_SAMPLES_PER_PIXEL, str(pixels.shape[2]))
elif size_c > 1:
p.channel_count = size_c
pixel_buffer = convert_pixels_to_buffer(pixels, pixel_type)
xml = omexml.to_xml()
script = """
importClass(Packages.loci.formats.services.OMEXMLService,
Packages.loci.common.services.ServiceFactory,
Packages.loci.formats.ImageWriter);
var service = new ServiceFactory().getInstance(OMEXMLService);
var metadata = service.createOMEXMLMetadata(xml);
var writer = new ImageWriter();
writer.setMetadataRetrieve(metadata);
writer.setId(path);
writer.setInterleaved(true);
writer.saveBytes(index, buffer);
writer.close();
"""
jutil.run_script(script, dict(path=pathname, xml=xml, index=index, buffer=pixel_buffer))
def get_context():
'''Get the ImageJ context
This is a singleton ImageJ context. We need a singleton for now because
of http://trac.imagej.net/ticket/1413
This is an imagej.ImageJ, which at one point was the context.
Call self.getContext() to get the org.scijava.Context which may be
what you want.
'''
global the_imagej_context
if the_imagej_context is None:
the_imagej_context = create_context(None)
#
# We have to turn off the updater and tell ImageJ to never call
# System.exit. We have to tell ImageJ that we read the readme file.
#
# To Do: programatically turn off the updater and take control of
# the quitting and exit process.
#
max_value = J.run_script(
"java.lang.Long.toString(java.lang.Long.MAX_VALUE);")
prefs = [("imagej.updater.core.UpToDate", "latestNag", max_value),
("imagej.core.options.OptionsMisc", "exitWhenQuitting",
"false")]
plugin_service = the_imagej_context.getService(
"org.scijava.plugin.PluginService")
ui_interface = J.class_for_name("imagej.ui.UserInterface")
script = """
var result = java.lang.System.getProperty('ij.ui');
if (! result) {
var infos = pluginService.getPluginsOfType(ui_interface);
if (infos.size() > 0) {
result = infos.get(0).getClassName();
}
}
result;"""
ui_class = J.run_script(
script,
dict(pluginService=plugin_service, ui_interface=ui_interface))
first_run = "firstRun-" + the_imagej_context.getVersion()
if ui_class:
prefs.append((ui_class, first_run, "false"))
for class_name, key, value in prefs:
c = J.class_for_name(class_name)
J.static_call(
"imagej/util/Prefs", "put",
"(Ljava/lang/Class;Ljava/lang/String;Ljava/lang/String;)V", c,
key, value)
return the_imagej_context
def get_context():
'''Get the ImageJ context
This is a singleton ImageJ context. We need a singleton for now because
of http://trac.imagej.net/ticket/1413
This is an imagej.ImageJ, which at one point was the context.
Call self.getContext() to get the org.scijava.Context which may be
what you want.
'''
global the_imagej_context
if the_imagej_context is None:
the_imagej_context = create_context(None)
#
# We have to turn off the updater and tell ImageJ to never call
# System.exit. We have to tell ImageJ that we read the readme file.
#
# To Do: programatically turn off the updater and take control of
# the quitting and exit process.
#
max_value = J.run_script(
"java.lang.Long.toString(java.lang.Long.MAX_VALUE);")
prefs = [
("imagej.updater.core.UpToDate", "latestNag", max_value),
("imagej.core.options.OptionsMisc", "exitWhenQuitting", "false")]
plugin_service = the_imagej_context.getService(
"org.scijava.plugin.PluginService")
ui_interface = J.class_for_name("imagej.ui.UserInterface")
script = """
var result = java.lang.System.getProperty('ij.ui');
if (! result) {
var infos = pluginService.getPluginsOfType(ui_interface);
if (infos.size() > 0) {
result = infos.get(0).getClassName();
}
}
result;"""
ui_class = J.run_script(script, dict(pluginService=plugin_service,
ui_interface=ui_interface))
first_run = "firstRun-"+the_imagej_context.getVersion()
if ui_class:
prefs.append((ui_class, first_run, "false"))
for class_name, key, value in prefs:
c = J.class_for_name(class_name)
J.static_call(
"imagej/util/Prefs", "put",
"(Ljava/lang/Class;Ljava/lang/String;Ljava/lang/String;)V",
c, key, value)
return the_imagej_context
def test_06_03_future_main(self):
c = J.run_script("""
new java.util.concurrent.Callable() {
call: function() { return 2+2; }};""")
result = J.execute_future_in_main_thread(
J.make_future_task(c, fn_post_process=J.unwrap_javascript))
self.assertEqual(result, 4)
def get_commands():
"""Return a list of the available command strings"""
script = """
new java.util.concurrent.Callable() {
call: function() {
importClass(Packages.ij.Menus, Packages.ij.IJ);
var hashtable=Menus.getCommands();
if (hashtable==null) {
IJ.run("pleaseignorethis");
hashtable = Menus.getCommands();
}
return hashtable;
}
};
"""
c = J.run_script(script, class_loader=get_user_loader())
hashtable = J.execute_callable_in_main_thread(c)
keys = J.call(hashtable, "keys", "()Ljava/util/Enumeration;")
keys = J.jenumeration_to_string_list(keys)
values = J.call(hashtable, "values", "()Ljava/util/Collection;")
values = [J.to_string(x) for x in J.iterate_java(J.call(values, "iterator", "()Ljava/util/Iterator;"))]
class CommandList(list):
def __init__(self):
super(CommandList, self).__init__(keys)
self.values = values
return CommandList()
def set_omero_credentials(omero_server, omero_port, omero_username, omero_password):
'''Set the credentials to be used to connect to the Omero server
omero_server - DNS name of the server
omero_port - use this port to connect to the server
omero_username - log on as this user
omero_password - log on using this password
The session ID is valid after this is called. An exception is thrown
if the login fails. omero_logout() can be called to log out.
'''
global __omero_server
global __omero_username
global __omero_session_id
global __omero_port
__omero_server = omero_server
__omero_port = omero_port
__omero_username = omero_username
script = """
var client = Packages.omero.client(server, port);
var serverFactory = client.createSession(user, password);
client.getSessionId();
"""
__omero_session_id = jutil.run_script(script, dict(
server = __omero_server,
port = __omero_port,
user = __omero_username,
password = omero_password))
return __omero_session_id
def test_06_03_future_main(self):
c = J.run_script("""
new java.util.concurrent.Callable() {
call: function() { return 2+2; }};""")
result = J.execute_future_in_main_thread(
J.make_future_task(c, fn_post_process=J.unwrap_javascript))
self.assertEqual(result, 4)
def set_omero_credentials(omero_server, omero_port, omero_username,
omero_password):
'''Set the credentials to be used to connect to the Omero server
omero_server - DNS name of the server
omero_port - use this port to connect to the server
omero_username - log on as this user
omero_password - log on using this password
The session ID is valid after this is called. An exception is thrown
if the login fails. omero_logout() can be called to log out.
'''
global __omero_server
global __omero_username
global __omero_session_id
global __omero_port
__omero_server = omero_server
__omero_port = omero_port
__omero_username = omero_username
script = """
var client = Packages.omero.client(server, port);
var serverFactory = client.createSession(user, password);
client.getSessionId();
"""
__omero_session_id = jutil.run_script(
script,
dict(server=__omero_server,
port=__omero_port,
user=__omero_username,
password=omero_password))
return __omero_session_id
def on_show_imagej(self):
"""Show the ImageJ user interface
This method shows the ImageJ user interface when the user presses
the Show ImageJ button.
"""
logger.debug("Starting ImageJ UI")
ui_service = ij2.get_ui_service(get_context())
if ui_service is not None and not ui_service.isVisible():
if cpprefs.get_headless():
# Silence the auto-updater in the headless preferences
#
ij2.update_never_remind()
ui_service.createUI()
elif ui_service is not None:
ui = ui_service.getDefaultUI()
J.execute_runnable_in_main_thread(
J.run_script(
"""new java.lang.Runnable() {
run: function() {
ui.getApplicationFrame().setVisible(true); }}""",
dict(ui=ui),
),
True,
)
def test_07_04_make_future_task_from_callable(self):
call_able = J.run_script("""
new java.util.concurrent.Callable() {
call: function() { return 2+2; }};""")
future = J.make_future_task(call_able,
fn_post_process=J.unwrap_javascript)
future.run()
self.assertEqual(future.get(), 4)
def set_current_image(imagej_obj):
'''Set the currently active window'''
imagej_obj.show()
image_window = imagej_obj.getWindow()
J.execute_runnable_in_main_thread(J.run_script(
"""new java.lang.Runnable() {
run:function() { Packages.ij.WindowManager.setCurrentWindow(w); }}
""", dict(w=image_window)), synchronous=True)
def test_07_04_make_future_task_from_callable(self):
call_able = J.run_script("""
new java.util.concurrent.Callable() {
call: function() { return 2+2; }};""")
future = J.make_future_task(call_able,
fn_post_process=J.unwrap_javascript)
future.run()
self.assertEqual(future.get(), 4)
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 createUIS(self, arg):
'''Create the ImageJ UI with a string argument'''
r = J.run_script(
"""new java.lang.Runnable() {
run:function() {
uiService.showUI(arg);
}
};
""", dict(uiService=self.o, arg=arg))
J.execute_runnable_in_main_thread(r, True)
def test_07_02_cancel_future(self):
future = J.run_script("""
new java.util.concurrent.FutureTask(
new java.util.concurrent.Callable() {
call: function() { return 2+2; }});""")
wfuture = J.get_future_wrapper(future,
fn_post_process=J.unwrap_javascript)
wfuture.cancel(True)
self.assertTrue(wfuture.isCancelled())
self.assertRaises(J.JavaException, wfuture.get)
def test_07_02_cancel_future(self):
future = J.run_script("""
new java.util.concurrent.FutureTask(
new java.util.concurrent.Callable() {
call: function() { return 2+2; }});""")
wfuture = J.get_future_wrapper(future,
fn_post_process=J.unwrap_javascript)
wfuture.cancel(True)
self.assertTrue(wfuture.isCancelled())
self.assertRaises(J.JavaException, wfuture.get)
def createUIS(self, arg):
'''Create the ImageJ UI with a string argument'''
r = J.run_script(
"""new java.lang.Runnable() {
run:function() {
uiService.showUI(arg);
}
};
""", dict(uiService=self.o, arg=arg))
J.execute_runnable_in_main_thread(r, True)
def __init__(self, path):
self.stream = None
if path.lower().startswith("omero:"):
self.rdr = get_omero_reader()
return
self.rdr = None
class_list = get_class_list()
find_rdr_script = """
var classes = class_list.getClasses();
var rdr = null;
var lc_filename = java.lang.String(filename.toLowerCase());
for (pass=0; pass < 3; pass++) {
for (class_idx in classes) {
var maybe_rdr = classes[class_idx].newInstance();
if (pass == 0) {
if (maybe_rdr.isThisType(filename, false)) {
rdr = maybe_rdr;
break;
}
continue;
} else if (pass == 1) {
var suffixes = maybe_rdr.getSuffixes();
var suffix_found = false;
for (suffix_idx in suffixes) {
var suffix = java.lang.String(suffixes[suffix_idx]);
suffix = suffix.toLowerCase();
if (lc_filename.endsWith(suffix)) {
suffix_found = true;
break;
}
}
if (! suffix_found) continue;
}
if (maybe_rdr.isThisType(stream)) {
rdr = maybe_rdr;
break;
}
}
if (rdr) break;
}
rdr;
"""
self.stream = jutil.make_instance(
'loci/common/RandomAccessInputStream', '(Ljava/lang/String;)V',
path)
filename = os.path.split(path)[1]
IFormatReader = make_iformat_reader_class()
jrdr = jutil.run_script(
find_rdr_script,
dict(class_list=class_list, filename=filename, stream=self.stream))
if jrdr is None:
raise ValueError("Could not find a Bio-Formats reader for %s",
path)
self.rdr = IFormatReader()
self.rdr.o = jrdr
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 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 = 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 get_pixel_data(self, axes = None):
imgplus = self.getImgPlus()
pixel_data = get_pixel_data(imgplus)
script = """
var result = java.util.ArrayList();
for (i=0;i<imgplus.numDimensions();i++) result.add(imgplus.axis(i));
result"""
inv_axes = J.run_script(script, dict(imgplus=imgplus))
inv_axes = list(J.iterate_collection(inv_axes))
transpose = calculate_transpose(inv_axes, axes)
return pixel_data.transpose(transpose)
def get_pixel_data(self, axes=None):
imgplus = self.getImgPlus()
pixel_data = get_pixel_data(imgplus)
script = """
var result = java.util.ArrayList();
for (i=0;i<imgplus.numDimensions();i++) result.add(imgplus.axis(i));
result"""
inv_axes = J.run_script(script, dict(imgplus=imgplus))
inv_axes = list(J.iterate_collection(inv_axes))
transpose = calculate_transpose(inv_axes, axes)
return pixel_data.transpose(transpose)
def get_temp_current_image():
'''Get the temporary ImagePlus object for the current thread'''
script = """
new java.util.concurrent.Callable() {
call: function() {
return Packages.ij.WindowManager.getTempCurrentImage();
}
};
"""
gtci = J.make_future_task(J.run_script(script))
imageplus_obj = J.execute_future_in_main_thread(gtci)
return get_imageplus_wrapper(imageplus_obj)
def __init__(self, path):
self.stream = None
if path.lower().startswith("omero:"):
self.rdr = get_omero_reader()
return
self.rdr = None
class_list = get_class_list()
find_rdr_script = """
var classes = class_list.getClasses();
var rdr = null;
var lc_filename = java.lang.String(filename.toLowerCase());
for (pass=0; pass < 3; pass++) {
for (class_idx in classes) {
var maybe_rdr = classes[class_idx].newInstance();
if (pass == 0) {
if (maybe_rdr.isThisType(filename, false)) {
rdr = maybe_rdr;
break;
}
continue;
} else if (pass == 1) {
var suffixes = maybe_rdr.getSuffixes();
var suffix_found = false;
for (suffix_idx in suffixes) {
var suffix = java.lang.String(suffixes[suffix_idx]);
suffix = suffix.toLowerCase();
if (lc_filename.endsWith(suffix)) {
suffix_found = true;
break;
}
}
if (! suffix_found) continue;
}
if (maybe_rdr.isThisType(stream)) {
rdr = maybe_rdr;
break;
}
}
if (rdr) break;
}
rdr;
"""
self.stream = jutil.make_instance('loci/common/RandomAccessInputStream',
'(Ljava/lang/String;)V', path)
filename = os.path.split(path)[1]
IFormatReader = make_iformat_reader_class()
jrdr = jutil.run_script(find_rdr_script, dict(class_list = class_list,
filename = filename,
stream = self.stream))
if jrdr is None:
raise ValueError("Could not find a Bio-Formats reader for %s", path)
self.rdr = IFormatReader()
self.rdr.o = jrdr
def test_07_01_wrap_future(self):
future = J.run_script("""
new java.util.concurrent.FutureTask(
new java.util.concurrent.Callable() {
call: function() { return 2+2; }});""")
wfuture = J.get_future_wrapper(future,
fn_post_process=J.unwrap_javascript)
self.assertFalse(wfuture.isDone())
self.assertFalse(wfuture.isCancelled())
wfuture.run()
self.assertTrue(wfuture.isDone())
self.assertEqual(wfuture.get(), 4)
def test_07_01_wrap_future(self):
future = J.run_script("""
new java.util.concurrent.FutureTask(
new java.util.concurrent.Callable() {
call: function() { return 2+2; }});""")
wfuture = J.get_future_wrapper(future,
fn_post_process=J.unwrap_javascript)
self.assertFalse(wfuture.isDone())
self.assertFalse(wfuture.isCancelled())
wfuture.run()
self.assertTrue(wfuture.isDone())
self.assertEqual(wfuture.get(), 4)
def fn(self, *args):
script = """
new java.util.concurrent.Callable() {
call: function() {
return o.%s(%s);
}
};
""" % (method, ",".join(["arg%d" % i for i in range(len(args))]))
d = dict([("arg%d" % i, arg) for i, arg in enumerate(args)])
d["o"] = self.o
future = J.make_future_task(J.run_script(script, d))
J.execute_future_in_main_thread(future)
return fn_post_process(future.get())
def show_imagej():
'''Show the ImageJ user interface'''
r = J.run_script("""new java.lang.Runnable() {
run: function() {
var imageJ = Packages.ij.IJ.getInstance();
if (imageJ == null) {
imageJ = Packages.ij.ImageJ();
}
imageJ.setVisible(true);
imageJ.toFront();
}
};""", class_loader=get_user_loader())
J.execute_runnable_in_main_thread(r, True)
def fn(self, *args):
script = """
new java.util.concurrent.Callable() {
call: function() {
return o.%s(%s);
}
};
""" % (method, ",".join(["arg%d" % i for i in range(len(args))]))
d = dict([("arg%d" % i, arg) for i, arg in enumerate(args)])
d["o"] = self.o
future = J.make_future_task(J.run_script(script, d))
J.execute_future_in_main_thread(future)
return fn_post_process(future.get())
def fn(self, *args):
script = """
new java.lang.Runnable() {
run: function() {
o.%s(%s);
}
};
""" % (method, ",".join(["arg%d" % i for i in range(len(args))]))
d = dict([("arg%d" % i, arg) for i, arg in enumerate(args)])
d["o"] = self.o
future = J.make_future_task(J.run_script(script, d))
J.execute_future_in_main_thread(future)
return future.get()
def fn(self, *args):
script = """
new java.lang.Runnable() {
run: function() {
o.%s(%s);
}
};
""" % (method, ",".join(["arg%d" % i for i in range(len(args))]))
d = dict([("arg%d" % i, arg) for i, arg in enumerate(args)])
d["o"] = self.o
future = J.make_future_task(J.run_script(script, d))
J.execute_future_in_main_thread(future)
return future.get()
def __init__(self):
if service_classes is None:
classes = None
ctxt_fn = J.run_script("""new java.util.concurrent.Callable() {
call: function() {
return new Packages.imagej.ImageJ(false);
}
}""")
else:
classes = [
J.class_for_name(x)
for x in service_classes or REQUIRED_SERVICES
]
classes = J.make_list(classes)
ctxt_fn = J.run_script(
"""new java.util.concurrent.Callable() {
call: function() {
return new Packages.imagej.ImageJ(classes);
}
}""", dict(classes=classes.o))
self.o = J.execute_future_in_main_thread(
J.make_future_task(ctxt_fn))
def createUI(self):
'''Create the ImageJ UI'''
#
# This has to be done via a future in order
# for CP to run the Mac event loop.
#
r = J.run_script(
"""new java.lang.Runnable() {
run:function() {
uiService.showUI();
}
};
""", dict(uiService=self.o))
J.execute_runnable_in_main_thread(r, True)
def __init__(self):
if service_classes is None:
classes = None
ctxt_fn = J.run_script(
"""new java.util.concurrent.Callable() {
call: function() {
return new Packages.imagej.ImageJ(false);
}
}""")
else:
classes = [
J.class_for_name(x)
for x in service_classes or REQUIRED_SERVICES]
classes = J.make_list(classes)
ctxt_fn = J.run_script(
"""new java.util.concurrent.Callable() {
call: function() {
return new Packages.imagej.ImageJ(classes);
}
}""", dict(classes = classes.o))
self.o = J.execute_future_in_main_thread(
J.make_future_task(ctxt_fn))
def createUI(self):
'''Create the ImageJ UI'''
#
# This has to be done via a future in order
# for CP to run the Mac event loop.
#
r = J.run_script(
"""new java.lang.Runnable() {
run:function() {
uiService.showUI();
}
};
""", dict(uiService=self.o))
J.execute_runnable_in_main_thread(r, True)
def run(self, workspace):
jb.attach()#initialize JVM
input_image_name = self.input_image_name.value
output_image_name = self.output_image_name.value
self.gsize = self.input_gaussian_filter.value
self.rsize = self.input_rolling_ball.value
self.lowseed = self.input_low_seed.value
self.highseed = self.input_high_seed.value
image_set = workspace.image_set
assert isinstance(image_set, cpi.ImageSet)
#prepare input image
input_image = image_set.get_image(input_image_name, must_be_grayscale = True)
input_pixels = input_image.pixel_data
ij_processor = ijiproc.make_image_processor((input_pixels*255.0).astype('float32'))
#JavaScript API
script = """
var img=Packages.ij.ImagePlus(name,ij_processor);
Packages.ij.IJ.run(img, "8-bit", "");
var macro="g_size="+gsize+" r_size="+rsize+" low_edge="+lowseed+" high_edge="+highseed+" noise=-1";
java.lang.System.out.println(macro);
Packages.ij.IJ.run(img, "Hysteresis Segment", macro);
var output_proc=img.getProcessor();
"""
#img.show();
#Packages.ij.WindowManager.setCurrentWindow(img.getWindow());
#"""
in_params={
"name":output_image_name,
"ij_processor": ij_processor,
"gsize":self.gsize,
"rsize":self.rsize,
"lowseed":self.lowseed,
"highseed":self.highseed}
out_params={"output_proc":None}
r = jb.run_script(script, bindings_in = in_params,bindings_out = out_params)
#prepare output image
output_pixels = ijiproc.get_image(out_params["output_proc"], False)
output_image = cpi.Image(output_pixels, parent_image = input_image)
#write output
image_set.add(output_image_name, output_image)
if workspace.frame is not None:
workspace.display_data.input_pixels = input_pixels
workspace.display_data.output_pixels = output_pixels
jb.detach()#close JVM
def inject_image(self, pixels, name=''):
'''inject an image into ImageJ for processing'''
ij_processor = ijiproc.make_image_processor(
(pixels * 255.0).astype('float32'))
script = """
new java.lang.Runnable() {
run: function() {
var imp = Packages.ij.ImagePlus(name, ij_processor);
imp.show();
Packages.ij.WindowManager.setCurrentWindow(imp.getWindow());
}};"""
r = J.run_script(script, bindings_in = {
"name":name,
"ij_processor": ij_processor})
J.execute_runnable_in_main_thread(r, True)
def test_05_06_create_dataset(self):
i,j = np.mgrid[:7, :9]
image = (i+j*10).astype(float)
ds = ij2.create_dataset(self.context, image, "Foo")
imgplus = ds.getImgPlus()
script = """
var ra=imgplus.randomAccess();
ra.setPosition(x, 0);
ra.setPosition(y, 1);
ra.get().get()"""
fn = np.frompyfunc(
lambda x, y: J.run_script(script,
dict(imgplus=imgplus, x=x, y=y)), 2, 1)
pixel_data = fn(j, i)
np.testing.assert_array_equal(image, pixel_data)
def createDisplay(self, name, dataset):
'''Create a display that contains the given dataset'''
#
# Must be run on the gui thread
#
jcallable = J.run_script(
"""new java.util.concurrent.Callable() {
call:function() {
return displayService.createDisplay(name, dataset);
}
};
""", dict(displayService=self.o, name=name, dataset=dataset.o))
future = J.make_future_task(jcallable,
fn_post_process=wrap_display)
return J.execute_future_in_main_thread(future)
def createDisplay(self, name, dataset):
"""Create a display that contains the given dataset"""
#
# Must be run on the gui thread
#
jcallable = J.run_script(
"""new java.util.concurrent.Callable() {
call:function() {
return displayService.createDisplay(name, dataset);
}
};
""",
dict(displayService=self.o, name=name, dataset=dataset.o),
)
future = J.make_future_task(jcallable, fn_post_process=wrap_display)
return J.execute_future_in_main_thread(future)
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 get_measurements_for_good_pipeline(nimages = 1,
group_numbers = None):
'''Get an appropriately initialized measurements structure for the good pipeline'''
path = os.path.join(example_images_directory(), "ExampleSBSImages")
m = cpmeas.Measurements()
if group_numbers is None:
group_numbers = [1] * nimages
group_indexes = [1]
last_group_number = group_numbers[0]
group_index = 1
for group_number in group_numbers:
if group_number == last_group_number:
group_index += 1
else:
group_index = 1
group_indexes.append(group_index)
for i in range(1, nimages+1):
filename = ("Channel2-%02d-%s-%02d.tif" %
(i, "ABCDEFGH"[int((i-1) / 12)], ((i-1) % 12) + 1))
url = pathname2url(os.path.join(path, filename))
m[cpmeas.IMAGE, cpmeas.C_FILE_NAME + "_DNA", i] = filename
m[cpmeas.IMAGE, cpmeas.C_PATH_NAME + "_DNA", i] = path
m[cpmeas.IMAGE, cpmeas.C_URL+"_DNA", i] = url
m[cpmeas.IMAGE, cpmeas.GROUP_NUMBER, i] = group_numbers[i-1]
m[cpmeas.IMAGE, cpmeas.GROUP_INDEX, i] = group_indexes[i-1]
jblob = J.run_script("""
importPackage(Packages.org.cellprofiler.imageset);
importPackage(Packages.org.cellprofiler.imageset.filter);
var imageFile=new ImageFile(new java.net.URI(url));
var imageFileDetails = new ImageFileDetails(imageFile);
var imageSeries=new ImageSeries(imageFile, 0);
var imageSeriesDetails = new ImageSeriesDetails(imageSeries, imageFileDetails);
var imagePlane=new ImagePlane(imageSeries, 0, ImagePlane.ALWAYS_MONOCHROME);
var ipd = new ImagePlaneDetails(imagePlane, imageSeriesDetails);
var stack = ImagePlaneDetailsStack.makeMonochromeStack(ipd);
var stacks = java.util.Collections.singletonList(stack);
var keys = java.util.Collections.singletonList(imageNumber);
var imageSet = new ImageSet(stacks, keys);
imageSet.compress(java.util.Collections.singletonList("DNA"), null);
""", dict(url=url, imageNumber = str(i)))
blob = J.get_env().get_byte_array_elements(jblob)
m[cpmeas.IMAGE, M_IMAGE_SET, i, blob.dtype] = blob
pipeline = cpp.Pipeline()
pipeline.loadtxt(StringIO(GOOD_PIPELINE))
pipeline.write_pipeline_measurement(m)
return m
def get_measurements_for_good_pipeline(nimages=1, group_numbers=None):
'''Get an appropriately initialized measurements structure for the good pipeline'''
path = os.path.join(example_images_directory(), "ExampleSBSImages")
m = cpmeas.Measurements()
if group_numbers is None:
group_numbers = [1] * nimages
group_indexes = [1]
last_group_number = group_numbers[0]
group_index = 1
for group_number in group_numbers:
if group_number == last_group_number:
group_index += 1
else:
group_index = 1
group_indexes.append(group_index)
for i in range(1, nimages + 1):
filename = ("Channel2-%02d-%s-%02d.tif" % (i, "ABCDEFGH"[int(
(i - 1) / 12)], ((i - 1) % 12) + 1))
url = pathname2url(os.path.join(path, filename))
m[cpmeas.IMAGE, cpmeas.C_FILE_NAME + "_DNA", i] = filename
m[cpmeas.IMAGE, cpmeas.C_PATH_NAME + "_DNA", i] = path
m[cpmeas.IMAGE, cpmeas.C_URL + "_DNA", i] = url
m[cpmeas.IMAGE, cpmeas.GROUP_NUMBER, i] = group_numbers[i - 1]
m[cpmeas.IMAGE, cpmeas.GROUP_INDEX, i] = group_indexes[i - 1]
jblob = J.run_script(
"""
importPackage(Packages.org.cellprofiler.imageset);
importPackage(Packages.org.cellprofiler.imageset.filter);
var imageFile=new ImageFile(new java.net.URI(url));
var imageFileDetails = new ImageFileDetails(imageFile);
var imageSeries=new ImageSeries(imageFile, 0);
var imageSeriesDetails = new ImageSeriesDetails(imageSeries, imageFileDetails);
var imagePlane=new ImagePlane(imageSeries, 0, ImagePlane.ALWAYS_MONOCHROME);
var ipd = new ImagePlaneDetails(imagePlane, imageSeriesDetails);
var stack = ImagePlaneDetailsStack.makeMonochromeStack(ipd);
var stacks = java.util.Collections.singletonList(stack);
var keys = java.util.Collections.singletonList(imageNumber);
var imageSet = new ImageSet(stacks, keys);
imageSet.compress(java.util.Collections.singletonList("DNA"), null);
""", dict(url=url, imageNumber=str(i)))
blob = J.get_env().get_byte_array_elements(jblob)
m[cpmeas.IMAGE, M_IMAGE_SET, i, blob.dtype] = blob
pipeline = cpp.Pipeline()
pipeline.loadtxt(StringIO(GOOD_PIPELINE))
pipeline.write_pipeline_measurement(m)
return m
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 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 get_current_image():
'''Get the WindowManager's current image
returns a wrapped ImagePlus object
'''
#
# Run this on the UI thread so its thread context is the same
# as the macro invocation
#
script = """
new java.util.concurrent.Callable() {
call: function() {
return Packages.ij.WindowManager.getCurrentImage();
}
};
"""
gci = J.make_future_task(J.run_script(script))
imageplus_obj = J.execute_future_in_main_thread(gci)
return get_imageplus_wrapper(imageplus_obj)
def run_batch_macro(macro_text, imp):
'''Run a macro in batch mode
macro_text - the macro program to be run
imp - an image plus to become the active image
returns the image plus that was the active image at the end of the run
'''
script = """
new java.util.concurrent.Callable() {
call: function() {
return interp.runBatchMacro(macro_text, imp);
}
};
"""
interp = J.make_instance("ij/macro/Interpreter", "()V")
future = J.make_future_task(
J.run_script(script, dict(interp=interp,
macro_text=macro_text,
imp=imp)))
return J.execute_future_in_main_thread(future)
def test_06_01_get_mask_data(self):
# Get the overlay data from a display
#
display_svc = ij2.get_display_service(self.context)
overlay_svc = ij2.get_overlay_service(self.context)
image = np.zeros((30, 30))
ds = ij2.create_dataset(self.context, image, "Foo")
display = display_svc.createDisplay("Foo", ds)
d2 = display_svc.createDisplay("Bar", ij2.create_dataset(self.context, image, "Bar"))
overlay = J.run_script(
"""var o = new Packages.imagej.data.overlay.RectangleOverlay(context.getContext());
o.setOrigin(5, 0);
o.setOrigin(3, 1);
o.setExtent(6, 0);
o.setExtent(7, 1);
o;""", dict(context=self.context))
overlay_svc.addOverlays(display, J.make_list([overlay]))
ij2.select_overlay(display.o, overlay)
mask = ij2.create_mask(display)
i, j = np.mgrid[0:mask.shape[0], 0:mask.shape[1]]
np.testing.assert_equal(mask, (j >= 5) & (j < 11) & (i >= 3) & (i < 10))
def get_omero_reader():
'''Return an loci.ome.io.OMEROReader instance, wrapped as a FormatReader'''
script = """
var rdr = new Packages.loci.ome.io.OmeroReader();
rdr.setServer(server);
rdr.setPort(port);
rdr.setUsername(username);
rdr.setSessionID(sessionID);
rdr;
"""
if __omero_session_id is None:
omero_login()
jrdr = jutil.run_script(
script,
dict(server=__omero_server,
port=__omero_port,
username=__omero_username,
sessionID=__omero_session_id))
rdr = make_iformat_reader_class()()
rdr.o = jrdr
return rdr
def on_show_imagej(self):
'''Show the ImageJ user interface
This method shows the ImageJ user interface when the user presses
the Show ImageJ button.
'''
logger.debug("Starting ImageJ UI")
ui_service = ij2.get_ui_service(get_context())
if ui_service is not None and not ui_service.isVisible():
if cpprefs.get_headless():
# Silence the auto-updater in the headless preferences
#
ij2.update_never_remind()
ui_service.createUI()
elif ui_service is not None:
ui = ui_service.getDefaultUI()
J.execute_runnable_in_main_thread(
J.run_script(
"""new java.lang.Runnable() {
run: function() {
ui.getApplicationFrame().setVisible(true); }}""",
dict(ui=ui)), True)
